log started: Sun Nov  1 20:52:15 2015

Log file: ./leap.log
>> #
>> # ----- leaprc for loading the ff12SB force field
>> # ----- NOTE: this is designed for PDB format 3!
>> #    Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA
>> #
>> #	load atom type hybridizations
>> #
>> addAtomTypes {
>> 	{ "H"   "H" "sp3" }
>> 	{ "HO"  "H" "sp3" }
>> 	{ "HS"  "H" "sp3" }
>> 	{ "H1"  "H" "sp3" }
>> 	{ "H2"  "H" "sp3" }
>> 	{ "H3"  "H" "sp3" }
>> 	{ "H4"  "H" "sp3" }
>> 	{ "H5"  "H" "sp3" }
>> 	{ "HW"  "H" "sp3" }
>> 	{ "HC"  "H" "sp3" }
>> 	{ "HA"  "H" "sp3" }
>> 	{ "HP"  "H" "sp3" }
>> 	{ "HZ"  "H" "sp3" }
>> 	{ "OH"  "O" "sp3" }
>> 	{ "OS"  "O" "sp3" }
>> 	{ "O"   "O" "sp2" }
>> 	{ "O2"  "O" "sp2" }
>> 	{ "OP"  "O" "sp2" }
>> 	{ "OW"  "O" "sp3" }
>> 	{ "CT"  "C" "sp3" }
>> 	{ "CX"  "C" "sp3" }
>> 	{ "C8"  "C" "sp3" }
>> 	{ "2C"  "C" "sp3" }
>> 	{ "3C"  "C" "sp3" }
>> 	{ "CH"  "C" "sp3" }
>> 	{ "CS"  "C" "sp2" }
>> 	{ "C"   "C" "sp2" }
>> 	{ "CO"   "C" "sp2" }
>> 	{ "C*"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CB"  "C" "sp2" }
>> 	{ "CC"  "C" "sp2" }
>> 	{ "CN"  "C" "sp2" }
>> 	{ "CM"  "C" "sp2" }
>> 	{ "CK"  "C" "sp2" }
>> 	{ "CQ"  "C" "sp2" }
>> 	{ "CD"  "C" "sp2" }
>> 	{ "C5"  "C" "sp2" }
>> 	{ "C4"  "C" "sp2" }
>> 	{ "CP"  "C" "sp2" }
>> 	{ "CI"  "C" "sp3" }
>> 	{ "CJ"  "C" "sp2" }
>> 	{ "CW"  "C" "sp2" }
>> 	{ "CV"  "C" "sp2" }
>> 	{ "CR"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CY"  "C" "sp2" }
>> 	{ "C0"  "Ca" "sp3" }
>> 	{ "MG"  "Mg" "sp3" }
>> 	{ "N"   "N" "sp2" }
>> 	{ "NA"  "N" "sp2" }
>> 	{ "N2"  "N" "sp2" }
>> 	{ "N*"  "N" "sp2" }
>> 	{ "NP"  "N" "sp2" }
>> 	{ "NQ"  "N" "sp2" }
>> 	{ "NB"  "N" "sp2" }
>> 	{ "NC"  "N" "sp2" }
>> 	{ "NT"  "N" "sp3" }
>> 	{ "NY"  "N" "sp2" }
>> 	{ "N3"  "N" "sp3" }
>> 	{ "S"   "S" "sp3" }
>> 	{ "SH"  "S" "sp3" }
>> 	{ "P"   "P" "sp3" }
>> 	{ "LP"  ""  "sp3" }
>> 	{ "EP"  ""  "sp3" }
>> 	{ "F"   "F" "sp3" }
>> 	{ "Cl"  "Cl" "sp3" }
>> 	{ "Br"  "Br" "sp3" }
>> 	{ "I"   "I"  "sp3" }
>> 	{ "F-"   "F" "sp3" }
>> 	{ "Cl-"  "Cl" "sp3" }
>> 	{ "Br-"  "Br" "sp3" }
>> 	{ "I-"   "I"  "sp3" }
>> 	{ "Li+"  "Li"  "sp3" }
>> 	{ "Na+"  "Na"  "sp3" }
>> 	{ "K+"  "K"  "sp3" }
>> 	{ "Rb+"  "Rb"  "sp3" }
>> 	{ "Cs+"  "Cs"  "sp3" }
>> 	{ "Mg+"  "Mg"  "sp3" }
>> # glycam
>> 	{ "OG"  "O" "sp3" }
>> 	{ "OL"  "O" "sp3" }
>> 	{ "AC"  "C" "sp3" }
>> 	{ "EC"  "C" "sp3" }
>> }
>> #
>> #	Load the main parameter set.
>> #
>> parm10 = loadamberparams parm10.dat
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
(UNKNOWN ATOM TYPE: Zn)
(UNKNOWN ATOM TYPE: EP)
>> frcmod12SB = loadamberparams frcmod.ff12SB
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff12SB
Reading force field modification type file (frcmod)
Reading title:
ff12SB protein backbone and sidechain parameters
>> #
>> #	Load main chain and terminating amino acid libraries, nucleic acids
>> #
>> loadOff amino12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/amino12.lib
Loading: ALA
Loading: ARG
Loading: ASH
Loading: ASN
Loading: ASP
Loading: CYM
Loading: CYS
Loading: CYX
Loading: GLH
Loading: GLN
Loading: GLU
Loading: GLY
Loading: HID
Loading: HIE
Loading: HIP
Loading: HYP
Loading: ILE
Loading: LEU
Loading: LYN
Loading: LYS
Loading: MET
Loading: PHE
Loading: PRO
Loading: SER
Loading: THR
Loading: TRP
Loading: TYR
Loading: VAL
>> loadOff aminoct12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminoct12.lib
Loading: CALA
Loading: CARG
Loading: CASN
Loading: CASP
Loading: CCYS
Loading: CCYX
Loading: CGLN
Loading: CGLU
Loading: CGLY
Loading: CHID
Loading: CHIE
Loading: CHIP
Loading: CHYP
Loading: CILE
Loading: CLEU
Loading: CLYS
Loading: CMET
Loading: CPHE
Loading: CPRO
Loading: CSER
Loading: CTHR
Loading: CTRP
Loading: CTYR
Loading: CVAL
Loading: NHE
Loading: NME
>> loadOff aminont12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminont12.lib
Loading: ACE
Loading: NALA
Loading: NARG
Loading: NASN
Loading: NASP
Loading: NCYS
Loading: NCYX
Loading: NGLN
Loading: NGLU
Loading: NGLY
Loading: NHID
Loading: NHIE
Loading: NHIP
Loading: NILE
Loading: NLEU
Loading: NLYS
Loading: NMET
Loading: NPHE
Loading: NPRO
Loading: NSER
Loading: NTHR
Loading: NTRP
Loading: NTYR
Loading: NVAL
>> loadOff nucleic12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/nucleic12.lib
Loading: A
Loading: A3
Loading: A5
Loading: AN
Loading: C
Loading: C3
Loading: C5
Loading: CN
Loading: DA
Loading: DA3
Loading: DA5
Loading: DAN
Loading: DC
Loading: DC3
Loading: DC5
Loading: DCN
Loading: DG
Loading: DG3
Loading: DG5
Loading: DGN
Loading: DT
Loading: DT3
Loading: DT5
Loading: DTN
Loading: G
Loading: G3
Loading: G5
Loading: GN
Loading: OHE
Loading: U
Loading: U3
Loading: U5
Loading: UN
>> #
>> #       Load water and ions
>> # 
>> loadOff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
>> loadOff solvents.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: MEOHBOX
Loading: NMABOX
Loading: OPC
Loading: OPCBOX
Loading: PL3
Loading: POL3BOX
Loading: QSPCFWBOX
Loading: SPC
Loading: SPCBOX
Loading: SPCFWBOX
Loading: SPF
Loading: SPG
Loading: T4E
Loading: TIP3PBOX
Loading: TIP3PFBOX
Loading: TIP4PBOX
Loading: TIP4PEWBOX
Loading: TIP5PBOX
Loading: TP3
Loading: TP4
Loading: TP5
Loading: TPF
>> HOH = TP3
>> WAT = TP3
>> 
>> #
>> #	Define the PDB name map for the amino acids and nucleic acids
>> #     (note: no NHYP!  use neutral form for now)
>> #
>> addPdbResMap {
>>   { 0 "HYP" "HYP"  } { 1 "HYP" "CHYP" }
>>   { 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
>>   { 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
>>   { 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
>>   { 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
>>   { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
>>   { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
>>   { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
>>   { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
>>   { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
>>   { 0 "HID" "NHID" } { 1 "HID" "CHID" }
>>   { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
>>   { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
>>   { 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
>>   { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
>>   { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
>>   { 0 "MET" "NMET" } { 1 "MET" "CMET" }
>>   { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
>>   { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
>>   { 0 "SER" "NSER" } { 1 "SER" "CSER" }
>>   { 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
>>   { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
>>   { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
>>   { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
>>   { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
>>   { 0 "G" "G5"  } { 1 "G" "G3"  } 
>>   { 0 "A" "A5"  } { 1 "A" "A3"  } 
>>   { 0 "C" "C5"  } { 1 "C" "C3"  } 
>>   { 0 "U" "U5"  } { 1 "U" "U3"  } 
>>   { 0 "DG" "DG5"  } { 1 "DG" "DG3"  }  
>>   { 0 "DA" "DA5"  } { 1 "DA" "DA3"  }  
>>   { 0 "DC" "DC5"  } { 1 "DC" "DC3"  }  
>>   { 0 "DT" "DT5"  } { 1 "DT" "DT3"  }  
>> #  some old Amber residue names for RNA:
>>   { 0  "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" }
>>   { 0  "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" }
>>   { 0  "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" }
>>   { 0  "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" }
>> #  some really old Amber residue names, assuming DNA:
>>   { 0 "GUA" "DG5"  } { 1 "GUA" "DG3"  } { "GUA" "DG" }
>>   { 0 "ADE" "DA5"  } { 1 "ADE" "DA3"  } { "ADE" "DA" }
>>   { 0 "CYT" "DC5"  } { 1 "CYT" "DC3"  } { "CYT" "DC" }
>>   { 0 "THY" "DT5"  } { 1 "THY" "DT3"  } { "THY" "DT" }
>> #  uncomment out the following if you have this old style RNA files:
>> # { 0 "GUA" "G5"  } { 1 "GUA" "G3"  } { "GUA" "G" }
>> # { 0 "ADE" "A5"  } { 1 "ADE" "A3"  } { "ADE" "A" }
>> # { 0 "CYT" "C5"  } { 1 "CYT" "C3"  } { "CYT" "C" }
>> # { 0 "URA" "R5"  } { 1 "URA" "R3"  } { "URA" "R" }
>> 
>> }
>> 
>> #  try to be good about reading in really old atom names as well:
>> addPdbAtomMap {
>>   { "O5*" "O5'" }
>>   { "C5*" "C5'" }
>>   { "C4*" "C4'" }
>>   { "O4*" "O4'" }
>>   { "C3*" "C3'" }
>>   { "O3*" "O3'" }
>>   { "C2*" "C2'" }
>>   { "O2*" "O2'" }
>>   { "C1*" "C1'" }
>>   { "C5M" "C7"  }
>>   { "H1*" "H1'" }
>>   { "H2*1" "H2'" }
>>   { "H2*2" "H2''" }
>>   { "HO*2" "HO2'" }
>>   { "H2'1" "H2'" }
>>   { "H2'2" "H2''" }
>>   { "H3*" "H3'" }
>>   { "H4*" "H4'" }
>>   { "H5*1" "H5'" }
>>   { "H5*2" "H5''" }
>>   { "H5'1" "H5'" }
>>   { "H5'2" "H5''" }
>>   { "HO'2" "HO2'" }
>>   { "H5T"  "HO5'" }
>>   { "H3T"  "HO3'" }
>>   { "O1'" "O4'" }
>>   { "OA"  "OP1" }
>>   { "OB"  "OP2" }
>>   { "O1P" "OP1" }
>>   { "O2P" "OP2" }
>> }
>> 
>> #
>> # assume that most often proteins use HIE
>> #
>> NHIS = NHIE
>> HIS = HIE
>> CHIS = CHIE
> 
> loadoff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
> loadamberparams frcmod.opc
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.opc
Reading force field modification type file (frcmod)
Reading title:
Parameters for OPC water (JPCL, 2014, 5 (21), pp 3863–3871) 
(UNKNOWN ATOM TYPE: EP)
> loadamberparams frcmod.ionsjc_tip4pew
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip4pew
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP4P/EW water from Joung & Cheatham JPCB (2008)
> 
> m = loadpdb init.pdb
Loading PDB file: ./init.pdb
Enter zPdbReadScan from call depth  0.
Exit  zPdbReadScan from call depth  0.
Matching PDB residue names to LEaP variables.
(Residue 0: A5, Terminal/beginning, was not found in name map.)
(Residue 1: C3, Terminal/last, was not found in name map.)
Joining A5 - C3
  total atoms in file: 63
> 
> 
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.131155 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<H4' 9>
Warning: Close contact of 1.307451 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<C4' 8>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> solvatebox m OPCBOX 8 iso
  Solute vdw bounding box:              12.265 11.150 10.292
  Total bounding box for atom centers:  28.265 28.265 28.265
      (box expansion for 'iso' is  11.9%)
  Solvent unit box:                     18.865 18.478 19.006
The number of boxes:  x= 2  y= 2  z= 2
Adding box at: x=0  y=0  z=0
Center of solvent box is: 9.432422, 9.239054, 9.503120
Adding box at: x=0  y=0  z=1
Center of solvent box is: 9.432422, 9.239054, -9.503120
Adding box at: x=0  y=1  z=0
Center of solvent box is: 9.432422, -9.239054, 9.503120
Adding box at: x=0  y=1  z=1
Center of solvent box is: 9.432422, -9.239054, -9.503120
Adding box at: x=1  y=0  z=0
Center of solvent box is: -9.432422, 9.239054, 9.503120
Adding box at: x=1  y=0  z=1
Center of solvent box is: -9.432422, 9.239054, -9.503120
Adding box at: x=1  y=1  z=0
Center of solvent box is: -9.432422, -9.239054, 9.503120
Adding box at: x=1  y=1  z=1
Center of solvent box is: -9.432422, -9.239054, -9.503120
  Volume: 31065.671 A^3 
  Total mass 11669.288 amu,  Density 0.624 g/cc
  Added 616 residues.
> quit
	Quit
log started: Sun Nov  1 20:52:15 2015

Log file: ./leap.log
>> #
>> # ----- leaprc for loading the ff12SB force field
>> # ----- NOTE: this is designed for PDB format 3!
>> #    Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA
>> #
>> #	load atom type hybridizations
>> #
>> addAtomTypes {
>> 	{ "H"   "H" "sp3" }
>> 	{ "HO"  "H" "sp3" }
>> 	{ "HS"  "H" "sp3" }
>> 	{ "H1"  "H" "sp3" }
>> 	{ "H2"  "H" "sp3" }
>> 	{ "H3"  "H" "sp3" }
>> 	{ "H4"  "H" "sp3" }
>> 	{ "H5"  "H" "sp3" }
>> 	{ "HW"  "H" "sp3" }
>> 	{ "HC"  "H" "sp3" }
>> 	{ "HA"  "H" "sp3" }
>> 	{ "HP"  "H" "sp3" }
>> 	{ "HZ"  "H" "sp3" }
>> 	{ "OH"  "O" "sp3" }
>> 	{ "OS"  "O" "sp3" }
>> 	{ "O"   "O" "sp2" }
>> 	{ "O2"  "O" "sp2" }
>> 	{ "OP"  "O" "sp2" }
>> 	{ "OW"  "O" "sp3" }
>> 	{ "CT"  "C" "sp3" }
>> 	{ "CX"  "C" "sp3" }
>> 	{ "C8"  "C" "sp3" }
>> 	{ "2C"  "C" "sp3" }
>> 	{ "3C"  "C" "sp3" }
>> 	{ "CH"  "C" "sp3" }
>> 	{ "CS"  "C" "sp2" }
>> 	{ "C"   "C" "sp2" }
>> 	{ "CO"   "C" "sp2" }
>> 	{ "C*"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CB"  "C" "sp2" }
>> 	{ "CC"  "C" "sp2" }
>> 	{ "CN"  "C" "sp2" }
>> 	{ "CM"  "C" "sp2" }
>> 	{ "CK"  "C" "sp2" }
>> 	{ "CQ"  "C" "sp2" }
>> 	{ "CD"  "C" "sp2" }
>> 	{ "C5"  "C" "sp2" }
>> 	{ "C4"  "C" "sp2" }
>> 	{ "CP"  "C" "sp2" }
>> 	{ "CI"  "C" "sp3" }
>> 	{ "CJ"  "C" "sp2" }
>> 	{ "CW"  "C" "sp2" }
>> 	{ "CV"  "C" "sp2" }
>> 	{ "CR"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CY"  "C" "sp2" }
>> 	{ "C0"  "Ca" "sp3" }
>> 	{ "MG"  "Mg" "sp3" }
>> 	{ "N"   "N" "sp2" }
>> 	{ "NA"  "N" "sp2" }
>> 	{ "N2"  "N" "sp2" }
>> 	{ "N*"  "N" "sp2" }
>> 	{ "NP"  "N" "sp2" }
>> 	{ "NQ"  "N" "sp2" }
>> 	{ "NB"  "N" "sp2" }
>> 	{ "NC"  "N" "sp2" }
>> 	{ "NT"  "N" "sp3" }
>> 	{ "NY"  "N" "sp2" }
>> 	{ "N3"  "N" "sp3" }
>> 	{ "S"   "S" "sp3" }
>> 	{ "SH"  "S" "sp3" }
>> 	{ "P"   "P" "sp3" }
>> 	{ "LP"  ""  "sp3" }
>> 	{ "EP"  ""  "sp3" }
>> 	{ "F"   "F" "sp3" }
>> 	{ "Cl"  "Cl" "sp3" }
>> 	{ "Br"  "Br" "sp3" }
>> 	{ "I"   "I"  "sp3" }
>> 	{ "F-"   "F" "sp3" }
>> 	{ "Cl-"  "Cl" "sp3" }
>> 	{ "Br-"  "Br" "sp3" }
>> 	{ "I-"   "I"  "sp3" }
>> 	{ "Li+"  "Li"  "sp3" }
>> 	{ "Na+"  "Na"  "sp3" }
>> 	{ "K+"  "K"  "sp3" }
>> 	{ "Rb+"  "Rb"  "sp3" }
>> 	{ "Cs+"  "Cs"  "sp3" }
>> 	{ "Mg+"  "Mg"  "sp3" }
>> # glycam
>> 	{ "OG"  "O" "sp3" }
>> 	{ "OL"  "O" "sp3" }
>> 	{ "AC"  "C" "sp3" }
>> 	{ "EC"  "C" "sp3" }
>> }
>> #
>> #	Load the main parameter set.
>> #
>> parm10 = loadamberparams parm10.dat
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
(UNKNOWN ATOM TYPE: Zn)
(UNKNOWN ATOM TYPE: EP)
>> frcmod12SB = loadamberparams frcmod.ff12SB
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff12SB
Reading force field modification type file (frcmod)
Reading title:
ff12SB protein backbone and sidechain parameters
>> #
>> #	Load main chain and terminating amino acid libraries, nucleic acids
>> #
>> loadOff amino12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/amino12.lib
Loading: ALA
Loading: ARG
Loading: ASH
Loading: ASN
Loading: ASP
Loading: CYM
Loading: CYS
Loading: CYX
Loading: GLH
Loading: GLN
Loading: GLU
Loading: GLY
Loading: HID
Loading: HIE
Loading: HIP
Loading: HYP
Loading: ILE
Loading: LEU
Loading: LYN
Loading: LYS
Loading: MET
Loading: PHE
Loading: PRO
Loading: SER
Loading: THR
Loading: TRP
Loading: TYR
Loading: VAL
>> loadOff aminoct12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminoct12.lib
Loading: CALA
Loading: CARG
Loading: CASN
Loading: CASP
Loading: CCYS
Loading: CCYX
Loading: CGLN
Loading: CGLU
Loading: CGLY
Loading: CHID
Loading: CHIE
Loading: CHIP
Loading: CHYP
Loading: CILE
Loading: CLEU
Loading: CLYS
Loading: CMET
Loading: CPHE
Loading: CPRO
Loading: CSER
Loading: CTHR
Loading: CTRP
Loading: CTYR
Loading: CVAL
Loading: NHE
Loading: NME
>> loadOff aminont12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminont12.lib
Loading: ACE
Loading: NALA
Loading: NARG
Loading: NASN
Loading: NASP
Loading: NCYS
Loading: NCYX
Loading: NGLN
Loading: NGLU
Loading: NGLY
Loading: NHID
Loading: NHIE
Loading: NHIP
Loading: NILE
Loading: NLEU
Loading: NLYS
Loading: NMET
Loading: NPHE
Loading: NPRO
Loading: NSER
Loading: NTHR
Loading: NTRP
Loading: NTYR
Loading: NVAL
>> loadOff nucleic12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/nucleic12.lib
Loading: A
Loading: A3
Loading: A5
Loading: AN
Loading: C
Loading: C3
Loading: C5
Loading: CN
Loading: DA
Loading: DA3
Loading: DA5
Loading: DAN
Loading: DC
Loading: DC3
Loading: DC5
Loading: DCN
Loading: DG
Loading: DG3
Loading: DG5
Loading: DGN
Loading: DT
Loading: DT3
Loading: DT5
Loading: DTN
Loading: G
Loading: G3
Loading: G5
Loading: GN
Loading: OHE
Loading: U
Loading: U3
Loading: U5
Loading: UN
>> #
>> #       Load water and ions
>> # 
>> loadOff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
>> loadOff solvents.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: MEOHBOX
Loading: NMABOX
Loading: OPC
Loading: OPCBOX
Loading: PL3
Loading: POL3BOX
Loading: QSPCFWBOX
Loading: SPC
Loading: SPCBOX
Loading: SPCFWBOX
Loading: SPF
Loading: SPG
Loading: T4E
Loading: TIP3PBOX
Loading: TIP3PFBOX
Loading: TIP4PBOX
Loading: TIP4PEWBOX
Loading: TIP5PBOX
Loading: TP3
Loading: TP4
Loading: TP5
Loading: TPF
>> HOH = TP3
>> WAT = TP3
>> 
>> #
>> #	Define the PDB name map for the amino acids and nucleic acids
>> #     (note: no NHYP!  use neutral form for now)
>> #
>> addPdbResMap {
>>   { 0 "HYP" "HYP"  } { 1 "HYP" "CHYP" }
>>   { 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
>>   { 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
>>   { 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
>>   { 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
>>   { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
>>   { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
>>   { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
>>   { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
>>   { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
>>   { 0 "HID" "NHID" } { 1 "HID" "CHID" }
>>   { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
>>   { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
>>   { 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
>>   { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
>>   { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
>>   { 0 "MET" "NMET" } { 1 "MET" "CMET" }
>>   { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
>>   { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
>>   { 0 "SER" "NSER" } { 1 "SER" "CSER" }
>>   { 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
>>   { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
>>   { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
>>   { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
>>   { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
>>   { 0 "G" "G5"  } { 1 "G" "G3"  } 
>>   { 0 "A" "A5"  } { 1 "A" "A3"  } 
>>   { 0 "C" "C5"  } { 1 "C" "C3"  } 
>>   { 0 "U" "U5"  } { 1 "U" "U3"  } 
>>   { 0 "DG" "DG5"  } { 1 "DG" "DG3"  }  
>>   { 0 "DA" "DA5"  } { 1 "DA" "DA3"  }  
>>   { 0 "DC" "DC5"  } { 1 "DC" "DC3"  }  
>>   { 0 "DT" "DT5"  } { 1 "DT" "DT3"  }  
>> #  some old Amber residue names for RNA:
>>   { 0  "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" }
>>   { 0  "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" }
>>   { 0  "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" }
>>   { 0  "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" }
>> #  some really old Amber residue names, assuming DNA:
>>   { 0 "GUA" "DG5"  } { 1 "GUA" "DG3"  } { "GUA" "DG" }
>>   { 0 "ADE" "DA5"  } { 1 "ADE" "DA3"  } { "ADE" "DA" }
>>   { 0 "CYT" "DC5"  } { 1 "CYT" "DC3"  } { "CYT" "DC" }
>>   { 0 "THY" "DT5"  } { 1 "THY" "DT3"  } { "THY" "DT" }
>> #  uncomment out the following if you have this old style RNA files:
>> # { 0 "GUA" "G5"  } { 1 "GUA" "G3"  } { "GUA" "G" }
>> # { 0 "ADE" "A5"  } { 1 "ADE" "A3"  } { "ADE" "A" }
>> # { 0 "CYT" "C5"  } { 1 "CYT" "C3"  } { "CYT" "C" }
>> # { 0 "URA" "R5"  } { 1 "URA" "R3"  } { "URA" "R" }
>> 
>> }
>> 
>> #  try to be good about reading in really old atom names as well:
>> addPdbAtomMap {
>>   { "O5*" "O5'" }
>>   { "C5*" "C5'" }
>>   { "C4*" "C4'" }
>>   { "O4*" "O4'" }
>>   { "C3*" "C3'" }
>>   { "O3*" "O3'" }
>>   { "C2*" "C2'" }
>>   { "O2*" "O2'" }
>>   { "C1*" "C1'" }
>>   { "C5M" "C7"  }
>>   { "H1*" "H1'" }
>>   { "H2*1" "H2'" }
>>   { "H2*2" "H2''" }
>>   { "HO*2" "HO2'" }
>>   { "H2'1" "H2'" }
>>   { "H2'2" "H2''" }
>>   { "H3*" "H3'" }
>>   { "H4*" "H4'" }
>>   { "H5*1" "H5'" }
>>   { "H5*2" "H5''" }
>>   { "H5'1" "H5'" }
>>   { "H5'2" "H5''" }
>>   { "HO'2" "HO2'" }
>>   { "H5T"  "HO5'" }
>>   { "H3T"  "HO3'" }
>>   { "O1'" "O4'" }
>>   { "OA"  "OP1" }
>>   { "OB"  "OP2" }
>>   { "O1P" "OP1" }
>>   { "O2P" "OP2" }
>> }
>> 
>> #
>> # assume that most often proteins use HIE
>> #
>> NHIS = NHIE
>> HIS = HIE
>> CHIS = CHIE
> 
> loadoff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
> loadamberparams frcmod.opc
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.opc
Reading force field modification type file (frcmod)
Reading title:
Parameters for OPC water (JPCL, 2014, 5 (21), pp 3863–3871) 
(UNKNOWN ATOM TYPE: EP)
> loadamberparams frcmod.ionsjc_tip4pew
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip4pew
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP4P/EW water from Joung & Cheatham JPCB (2008)
> 
> m = loadpdb init.pdb
Loading PDB file: ./init.pdb
Enter zPdbReadScan from call depth  0.
Exit  zPdbReadScan from call depth  0.
Matching PDB residue names to LEaP variables.
(Residue 0: A5, Terminal/beginning, was not found in name map.)
(Residue 1: C3, Terminal/last, was not found in name map.)
Joining A5 - C3
  total atoms in file: 63
> 
> 
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.131155 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<H4' 9>
Warning: Close contact of 1.307451 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<C4' 8>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> solvatebox m OPCBOX 9 iso
  Solute vdw bounding box:              12.265 11.150 10.292
  Total bounding box for atom centers:  30.265 30.265 30.265
      (box expansion for 'iso' is  11.1%)
  Solvent unit box:                     18.865 18.478 19.006
The number of boxes:  x= 2  y= 2  z= 2
Adding box at: x=0  y=0  z=0
Center of solvent box is: 9.432422, 9.239054, 9.503120
Adding box at: x=0  y=0  z=1
Center of solvent box is: 9.432422, 9.239054, -9.503120
Adding box at: x=0  y=1  z=0
Center of solvent box is: 9.432422, -9.239054, 9.503120
Adding box at: x=0  y=1  z=1
Center of solvent box is: 9.432422, -9.239054, -9.503120
Adding box at: x=1  y=0  z=0
Center of solvent box is: -9.432422, 9.239054, 9.503120
Adding box at: x=1  y=0  z=1
Center of solvent box is: -9.432422, 9.239054, -9.503120
Adding box at: x=1  y=1  z=0
Center of solvent box is: -9.432422, -9.239054, 9.503120
Adding box at: x=1  y=1  z=1
Center of solvent box is: -9.432422, -9.239054, -9.503120
  Volume: 37395.089 A^3 
  Total mass 14713.992 amu,  Density 0.653 g/cc
  Added 785 residues.
> quit
	Quit
log started: Sun Nov  1 20:52:15 2015

Log file: ./leap.log
>> #
>> # ----- leaprc for loading the ff12SB force field
>> # ----- NOTE: this is designed for PDB format 3!
>> #    Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA
>> #
>> #	load atom type hybridizations
>> #
>> addAtomTypes {
>> 	{ "H"   "H" "sp3" }
>> 	{ "HO"  "H" "sp3" }
>> 	{ "HS"  "H" "sp3" }
>> 	{ "H1"  "H" "sp3" }
>> 	{ "H2"  "H" "sp3" }
>> 	{ "H3"  "H" "sp3" }
>> 	{ "H4"  "H" "sp3" }
>> 	{ "H5"  "H" "sp3" }
>> 	{ "HW"  "H" "sp3" }
>> 	{ "HC"  "H" "sp3" }
>> 	{ "HA"  "H" "sp3" }
>> 	{ "HP"  "H" "sp3" }
>> 	{ "HZ"  "H" "sp3" }
>> 	{ "OH"  "O" "sp3" }
>> 	{ "OS"  "O" "sp3" }
>> 	{ "O"   "O" "sp2" }
>> 	{ "O2"  "O" "sp2" }
>> 	{ "OP"  "O" "sp2" }
>> 	{ "OW"  "O" "sp3" }
>> 	{ "CT"  "C" "sp3" }
>> 	{ "CX"  "C" "sp3" }
>> 	{ "C8"  "C" "sp3" }
>> 	{ "2C"  "C" "sp3" }
>> 	{ "3C"  "C" "sp3" }
>> 	{ "CH"  "C" "sp3" }
>> 	{ "CS"  "C" "sp2" }
>> 	{ "C"   "C" "sp2" }
>> 	{ "CO"   "C" "sp2" }
>> 	{ "C*"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CB"  "C" "sp2" }
>> 	{ "CC"  "C" "sp2" }
>> 	{ "CN"  "C" "sp2" }
>> 	{ "CM"  "C" "sp2" }
>> 	{ "CK"  "C" "sp2" }
>> 	{ "CQ"  "C" "sp2" }
>> 	{ "CD"  "C" "sp2" }
>> 	{ "C5"  "C" "sp2" }
>> 	{ "C4"  "C" "sp2" }
>> 	{ "CP"  "C" "sp2" }
>> 	{ "CI"  "C" "sp3" }
>> 	{ "CJ"  "C" "sp2" }
>> 	{ "CW"  "C" "sp2" }
>> 	{ "CV"  "C" "sp2" }
>> 	{ "CR"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CY"  "C" "sp2" }
>> 	{ "C0"  "Ca" "sp3" }
>> 	{ "MG"  "Mg" "sp3" }
>> 	{ "N"   "N" "sp2" }
>> 	{ "NA"  "N" "sp2" }
>> 	{ "N2"  "N" "sp2" }
>> 	{ "N*"  "N" "sp2" }
>> 	{ "NP"  "N" "sp2" }
>> 	{ "NQ"  "N" "sp2" }
>> 	{ "NB"  "N" "sp2" }
>> 	{ "NC"  "N" "sp2" }
>> 	{ "NT"  "N" "sp3" }
>> 	{ "NY"  "N" "sp2" }
>> 	{ "N3"  "N" "sp3" }
>> 	{ "S"   "S" "sp3" }
>> 	{ "SH"  "S" "sp3" }
>> 	{ "P"   "P" "sp3" }
>> 	{ "LP"  ""  "sp3" }
>> 	{ "EP"  ""  "sp3" }
>> 	{ "F"   "F" "sp3" }
>> 	{ "Cl"  "Cl" "sp3" }
>> 	{ "Br"  "Br" "sp3" }
>> 	{ "I"   "I"  "sp3" }
>> 	{ "F-"   "F" "sp3" }
>> 	{ "Cl-"  "Cl" "sp3" }
>> 	{ "Br-"  "Br" "sp3" }
>> 	{ "I-"   "I"  "sp3" }
>> 	{ "Li+"  "Li"  "sp3" }
>> 	{ "Na+"  "Na"  "sp3" }
>> 	{ "K+"  "K"  "sp3" }
>> 	{ "Rb+"  "Rb"  "sp3" }
>> 	{ "Cs+"  "Cs"  "sp3" }
>> 	{ "Mg+"  "Mg"  "sp3" }
>> # glycam
>> 	{ "OG"  "O" "sp3" }
>> 	{ "OL"  "O" "sp3" }
>> 	{ "AC"  "C" "sp3" }
>> 	{ "EC"  "C" "sp3" }
>> }
>> #
>> #	Load the main parameter set.
>> #
>> parm10 = loadamberparams parm10.dat
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
(UNKNOWN ATOM TYPE: Zn)
(UNKNOWN ATOM TYPE: EP)
>> frcmod12SB = loadamberparams frcmod.ff12SB
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff12SB
Reading force field modification type file (frcmod)
Reading title:
ff12SB protein backbone and sidechain parameters
>> #
>> #	Load main chain and terminating amino acid libraries, nucleic acids
>> #
>> loadOff amino12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/amino12.lib
Loading: ALA
Loading: ARG
Loading: ASH
Loading: ASN
Loading: ASP
Loading: CYM
Loading: CYS
Loading: CYX
Loading: GLH
Loading: GLN
Loading: GLU
Loading: GLY
Loading: HID
Loading: HIE
Loading: HIP
Loading: HYP
Loading: ILE
Loading: LEU
Loading: LYN
Loading: LYS
Loading: MET
Loading: PHE
Loading: PRO
Loading: SER
Loading: THR
Loading: TRP
Loading: TYR
Loading: VAL
>> loadOff aminoct12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminoct12.lib
Loading: CALA
Loading: CARG
Loading: CASN
Loading: CASP
Loading: CCYS
Loading: CCYX
Loading: CGLN
Loading: CGLU
Loading: CGLY
Loading: CHID
Loading: CHIE
Loading: CHIP
Loading: CHYP
Loading: CILE
Loading: CLEU
Loading: CLYS
Loading: CMET
Loading: CPHE
Loading: CPRO
Loading: CSER
Loading: CTHR
Loading: CTRP
Loading: CTYR
Loading: CVAL
Loading: NHE
Loading: NME
>> loadOff aminont12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminont12.lib
Loading: ACE
Loading: NALA
Loading: NARG
Loading: NASN
Loading: NASP
Loading: NCYS
Loading: NCYX
Loading: NGLN
Loading: NGLU
Loading: NGLY
Loading: NHID
Loading: NHIE
Loading: NHIP
Loading: NILE
Loading: NLEU
Loading: NLYS
Loading: NMET
Loading: NPHE
Loading: NPRO
Loading: NSER
Loading: NTHR
Loading: NTRP
Loading: NTYR
Loading: NVAL
>> loadOff nucleic12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/nucleic12.lib
Loading: A
Loading: A3
Loading: A5
Loading: AN
Loading: C
Loading: C3
Loading: C5
Loading: CN
Loading: DA
Loading: DA3
Loading: DA5
Loading: DAN
Loading: DC
Loading: DC3
Loading: DC5
Loading: DCN
Loading: DG
Loading: DG3
Loading: DG5
Loading: DGN
Loading: DT
Loading: DT3
Loading: DT5
Loading: DTN
Loading: G
Loading: G3
Loading: G5
Loading: GN
Loading: OHE
Loading: U
Loading: U3
Loading: U5
Loading: UN
>> #
>> #       Load water and ions
>> # 
>> loadOff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
>> loadOff solvents.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: MEOHBOX
Loading: NMABOX
Loading: OPC
Loading: OPCBOX
Loading: PL3
Loading: POL3BOX
Loading: QSPCFWBOX
Loading: SPC
Loading: SPCBOX
Loading: SPCFWBOX
Loading: SPF
Loading: SPG
Loading: T4E
Loading: TIP3PBOX
Loading: TIP3PFBOX
Loading: TIP4PBOX
Loading: TIP4PEWBOX
Loading: TIP5PBOX
Loading: TP3
Loading: TP4
Loading: TP5
Loading: TPF
>> HOH = TP3
>> WAT = TP3
>> 
>> #
>> #	Define the PDB name map for the amino acids and nucleic acids
>> #     (note: no NHYP!  use neutral form for now)
>> #
>> addPdbResMap {
>>   { 0 "HYP" "HYP"  } { 1 "HYP" "CHYP" }
>>   { 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
>>   { 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
>>   { 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
>>   { 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
>>   { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
>>   { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
>>   { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
>>   { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
>>   { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
>>   { 0 "HID" "NHID" } { 1 "HID" "CHID" }
>>   { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
>>   { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
>>   { 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
>>   { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
>>   { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
>>   { 0 "MET" "NMET" } { 1 "MET" "CMET" }
>>   { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
>>   { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
>>   { 0 "SER" "NSER" } { 1 "SER" "CSER" }
>>   { 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
>>   { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
>>   { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
>>   { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
>>   { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
>>   { 0 "G" "G5"  } { 1 "G" "G3"  } 
>>   { 0 "A" "A5"  } { 1 "A" "A3"  } 
>>   { 0 "C" "C5"  } { 1 "C" "C3"  } 
>>   { 0 "U" "U5"  } { 1 "U" "U3"  } 
>>   { 0 "DG" "DG5"  } { 1 "DG" "DG3"  }  
>>   { 0 "DA" "DA5"  } { 1 "DA" "DA3"  }  
>>   { 0 "DC" "DC5"  } { 1 "DC" "DC3"  }  
>>   { 0 "DT" "DT5"  } { 1 "DT" "DT3"  }  
>> #  some old Amber residue names for RNA:
>>   { 0  "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" }
>>   { 0  "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" }
>>   { 0  "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" }
>>   { 0  "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" }
>> #  some really old Amber residue names, assuming DNA:
>>   { 0 "GUA" "DG5"  } { 1 "GUA" "DG3"  } { "GUA" "DG" }
>>   { 0 "ADE" "DA5"  } { 1 "ADE" "DA3"  } { "ADE" "DA" }
>>   { 0 "CYT" "DC5"  } { 1 "CYT" "DC3"  } { "CYT" "DC" }
>>   { 0 "THY" "DT5"  } { 1 "THY" "DT3"  } { "THY" "DT" }
>> #  uncomment out the following if you have this old style RNA files:
>> # { 0 "GUA" "G5"  } { 1 "GUA" "G3"  } { "GUA" "G" }
>> # { 0 "ADE" "A5"  } { 1 "ADE" "A3"  } { "ADE" "A" }
>> # { 0 "CYT" "C5"  } { 1 "CYT" "C3"  } { "CYT" "C" }
>> # { 0 "URA" "R5"  } { 1 "URA" "R3"  } { "URA" "R" }
>> 
>> }
>> 
>> #  try to be good about reading in really old atom names as well:
>> addPdbAtomMap {
>>   { "O5*" "O5'" }
>>   { "C5*" "C5'" }
>>   { "C4*" "C4'" }
>>   { "O4*" "O4'" }
>>   { "C3*" "C3'" }
>>   { "O3*" "O3'" }
>>   { "C2*" "C2'" }
>>   { "O2*" "O2'" }
>>   { "C1*" "C1'" }
>>   { "C5M" "C7"  }
>>   { "H1*" "H1'" }
>>   { "H2*1" "H2'" }
>>   { "H2*2" "H2''" }
>>   { "HO*2" "HO2'" }
>>   { "H2'1" "H2'" }
>>   { "H2'2" "H2''" }
>>   { "H3*" "H3'" }
>>   { "H4*" "H4'" }
>>   { "H5*1" "H5'" }
>>   { "H5*2" "H5''" }
>>   { "H5'1" "H5'" }
>>   { "H5'2" "H5''" }
>>   { "HO'2" "HO2'" }
>>   { "H5T"  "HO5'" }
>>   { "H3T"  "HO3'" }
>>   { "O1'" "O4'" }
>>   { "OA"  "OP1" }
>>   { "OB"  "OP2" }
>>   { "O1P" "OP1" }
>>   { "O2P" "OP2" }
>> }
>> 
>> #
>> # assume that most often proteins use HIE
>> #
>> NHIS = NHIE
>> HIS = HIE
>> CHIS = CHIE
> 
> loadoff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
> loadamberparams frcmod.opc
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.opc
Reading force field modification type file (frcmod)
Reading title:
Parameters for OPC water (JPCL, 2014, 5 (21), pp 3863–3871) 
(UNKNOWN ATOM TYPE: EP)
> loadamberparams frcmod.ionsjc_tip4pew
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip4pew
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP4P/EW water from Joung & Cheatham JPCB (2008)
> 
> m = loadpdb init.pdb
Loading PDB file: ./init.pdb
Enter zPdbReadScan from call depth  0.
Exit  zPdbReadScan from call depth  0.
Matching PDB residue names to LEaP variables.
(Residue 0: A5, Terminal/beginning, was not found in name map.)
(Residue 1: C3, Terminal/last, was not found in name map.)
Joining A5 - C3
  total atoms in file: 63
> 
> 
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.131155 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<H4' 9>
Warning: Close contact of 1.307451 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<C4' 8>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> solvatebox m OPCBOX 10 iso
  Solute vdw bounding box:              12.265 11.150 10.292
  Total bounding box for atom centers:  32.265 32.265 32.265
      (box expansion for 'iso' is  10.3%)
  Solvent unit box:                     18.865 18.478 19.006
The number of boxes:  x= 2  y= 2  z= 2
Adding box at: x=0  y=0  z=0
Center of solvent box is: 9.432422, 9.239054, 9.503120
Adding box at: x=0  y=0  z=1
Center of solvent box is: 9.432422, 9.239054, -9.503120
Adding box at: x=0  y=1  z=0
Center of solvent box is: 9.432422, -9.239054, 9.503120
Adding box at: x=0  y=1  z=1
Center of solvent box is: 9.432422, -9.239054, -9.503120
Adding box at: x=1  y=0  z=0
Center of solvent box is: -9.432422, 9.239054, 9.503120
Adding box at: x=1  y=0  z=1
Center of solvent box is: -9.432422, 9.239054, -9.503120
Adding box at: x=1  y=1  z=0
Center of solvent box is: -9.432422, -9.239054, 9.503120
Adding box at: x=1  y=1  z=1
Center of solvent box is: -9.432422, -9.239054, -9.503120
  Volume: 44008.365 A^3 
  Total mass 17758.696 amu,  Density 0.670 g/cc
  Added 954 residues.
> quit
	Quit
log started: Sun Nov  1 20:52:15 2015

Log file: ./leap.log
>> #
>> # ----- leaprc for loading the ff12SB force field
>> # ----- NOTE: this is designed for PDB format 3!
>> #    Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA
>> #
>> #	load atom type hybridizations
>> #
>> addAtomTypes {
>> 	{ "H"   "H" "sp3" }
>> 	{ "HO"  "H" "sp3" }
>> 	{ "HS"  "H" "sp3" }
>> 	{ "H1"  "H" "sp3" }
>> 	{ "H2"  "H" "sp3" }
>> 	{ "H3"  "H" "sp3" }
>> 	{ "H4"  "H" "sp3" }
>> 	{ "H5"  "H" "sp3" }
>> 	{ "HW"  "H" "sp3" }
>> 	{ "HC"  "H" "sp3" }
>> 	{ "HA"  "H" "sp3" }
>> 	{ "HP"  "H" "sp3" }
>> 	{ "HZ"  "H" "sp3" }
>> 	{ "OH"  "O" "sp3" }
>> 	{ "OS"  "O" "sp3" }
>> 	{ "O"   "O" "sp2" }
>> 	{ "O2"  "O" "sp2" }
>> 	{ "OP"  "O" "sp2" }
>> 	{ "OW"  "O" "sp3" }
>> 	{ "CT"  "C" "sp3" }
>> 	{ "CX"  "C" "sp3" }
>> 	{ "C8"  "C" "sp3" }
>> 	{ "2C"  "C" "sp3" }
>> 	{ "3C"  "C" "sp3" }
>> 	{ "CH"  "C" "sp3" }
>> 	{ "CS"  "C" "sp2" }
>> 	{ "C"   "C" "sp2" }
>> 	{ "CO"   "C" "sp2" }
>> 	{ "C*"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CB"  "C" "sp2" }
>> 	{ "CC"  "C" "sp2" }
>> 	{ "CN"  "C" "sp2" }
>> 	{ "CM"  "C" "sp2" }
>> 	{ "CK"  "C" "sp2" }
>> 	{ "CQ"  "C" "sp2" }
>> 	{ "CD"  "C" "sp2" }
>> 	{ "C5"  "C" "sp2" }
>> 	{ "C4"  "C" "sp2" }
>> 	{ "CP"  "C" "sp2" }
>> 	{ "CI"  "C" "sp3" }
>> 	{ "CJ"  "C" "sp2" }
>> 	{ "CW"  "C" "sp2" }
>> 	{ "CV"  "C" "sp2" }
>> 	{ "CR"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CY"  "C" "sp2" }
>> 	{ "C0"  "Ca" "sp3" }
>> 	{ "MG"  "Mg" "sp3" }
>> 	{ "N"   "N" "sp2" }
>> 	{ "NA"  "N" "sp2" }
>> 	{ "N2"  "N" "sp2" }
>> 	{ "N*"  "N" "sp2" }
>> 	{ "NP"  "N" "sp2" }
>> 	{ "NQ"  "N" "sp2" }
>> 	{ "NB"  "N" "sp2" }
>> 	{ "NC"  "N" "sp2" }
>> 	{ "NT"  "N" "sp3" }
>> 	{ "NY"  "N" "sp2" }
>> 	{ "N3"  "N" "sp3" }
>> 	{ "S"   "S" "sp3" }
>> 	{ "SH"  "S" "sp3" }
>> 	{ "P"   "P" "sp3" }
>> 	{ "LP"  ""  "sp3" }
>> 	{ "EP"  ""  "sp3" }
>> 	{ "F"   "F" "sp3" }
>> 	{ "Cl"  "Cl" "sp3" }
>> 	{ "Br"  "Br" "sp3" }
>> 	{ "I"   "I"  "sp3" }
>> 	{ "F-"   "F" "sp3" }
>> 	{ "Cl-"  "Cl" "sp3" }
>> 	{ "Br-"  "Br" "sp3" }
>> 	{ "I-"   "I"  "sp3" }
>> 	{ "Li+"  "Li"  "sp3" }
>> 	{ "Na+"  "Na"  "sp3" }
>> 	{ "K+"  "K"  "sp3" }
>> 	{ "Rb+"  "Rb"  "sp3" }
>> 	{ "Cs+"  "Cs"  "sp3" }
>> 	{ "Mg+"  "Mg"  "sp3" }
>> # glycam
>> 	{ "OG"  "O" "sp3" }
>> 	{ "OL"  "O" "sp3" }
>> 	{ "AC"  "C" "sp3" }
>> 	{ "EC"  "C" "sp3" }
>> }
>> #
>> #	Load the main parameter set.
>> #
>> parm10 = loadamberparams parm10.dat
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
(UNKNOWN ATOM TYPE: Zn)
(UNKNOWN ATOM TYPE: EP)
>> frcmod12SB = loadamberparams frcmod.ff12SB
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff12SB
Reading force field modification type file (frcmod)
Reading title:
ff12SB protein backbone and sidechain parameters
>> #
>> #	Load main chain and terminating amino acid libraries, nucleic acids
>> #
>> loadOff amino12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/amino12.lib
Loading: ALA
Loading: ARG
Loading: ASH
Loading: ASN
Loading: ASP
Loading: CYM
Loading: CYS
Loading: CYX
Loading: GLH
Loading: GLN
Loading: GLU
Loading: GLY
Loading: HID
Loading: HIE
Loading: HIP
Loading: HYP
Loading: ILE
Loading: LEU
Loading: LYN
Loading: LYS
Loading: MET
Loading: PHE
Loading: PRO
Loading: SER
Loading: THR
Loading: TRP
Loading: TYR
Loading: VAL
>> loadOff aminoct12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminoct12.lib
Loading: CALA
Loading: CARG
Loading: CASN
Loading: CASP
Loading: CCYS
Loading: CCYX
Loading: CGLN
Loading: CGLU
Loading: CGLY
Loading: CHID
Loading: CHIE
Loading: CHIP
Loading: CHYP
Loading: CILE
Loading: CLEU
Loading: CLYS
Loading: CMET
Loading: CPHE
Loading: CPRO
Loading: CSER
Loading: CTHR
Loading: CTRP
Loading: CTYR
Loading: CVAL
Loading: NHE
Loading: NME
>> loadOff aminont12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminont12.lib
Loading: ACE
Loading: NALA
Loading: NARG
Loading: NASN
Loading: NASP
Loading: NCYS
Loading: NCYX
Loading: NGLN
Loading: NGLU
Loading: NGLY
Loading: NHID
Loading: NHIE
Loading: NHIP
Loading: NILE
Loading: NLEU
Loading: NLYS
Loading: NMET
Loading: NPHE
Loading: NPRO
Loading: NSER
Loading: NTHR
Loading: NTRP
Loading: NTYR
Loading: NVAL
>> loadOff nucleic12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/nucleic12.lib
Loading: A
Loading: A3
Loading: A5
Loading: AN
Loading: C
Loading: C3
Loading: C5
Loading: CN
Loading: DA
Loading: DA3
Loading: DA5
Loading: DAN
Loading: DC
Loading: DC3
Loading: DC5
Loading: DCN
Loading: DG
Loading: DG3
Loading: DG5
Loading: DGN
Loading: DT
Loading: DT3
Loading: DT5
Loading: DTN
Loading: G
Loading: G3
Loading: G5
Loading: GN
Loading: OHE
Loading: U
Loading: U3
Loading: U5
Loading: UN
>> #
>> #       Load water and ions
>> # 
>> loadOff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
>> loadOff solvents.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: MEOHBOX
Loading: NMABOX
Loading: OPC
Loading: OPCBOX
Loading: PL3
Loading: POL3BOX
Loading: QSPCFWBOX
Loading: SPC
Loading: SPCBOX
Loading: SPCFWBOX
Loading: SPF
Loading: SPG
Loading: T4E
Loading: TIP3PBOX
Loading: TIP3PFBOX
Loading: TIP4PBOX
Loading: TIP4PEWBOX
Loading: TIP5PBOX
Loading: TP3
Loading: TP4
Loading: TP5
Loading: TPF
>> HOH = TP3
>> WAT = TP3
>> 
>> #
>> #	Define the PDB name map for the amino acids and nucleic acids
>> #     (note: no NHYP!  use neutral form for now)
>> #
>> addPdbResMap {
>>   { 0 "HYP" "HYP"  } { 1 "HYP" "CHYP" }
>>   { 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
>>   { 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
>>   { 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
>>   { 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
>>   { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
>>   { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
>>   { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
>>   { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
>>   { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
>>   { 0 "HID" "NHID" } { 1 "HID" "CHID" }
>>   { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
>>   { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
>>   { 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
>>   { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
>>   { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
>>   { 0 "MET" "NMET" } { 1 "MET" "CMET" }
>>   { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
>>   { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
>>   { 0 "SER" "NSER" } { 1 "SER" "CSER" }
>>   { 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
>>   { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
>>   { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
>>   { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
>>   { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
>>   { 0 "G" "G5"  } { 1 "G" "G3"  } 
>>   { 0 "A" "A5"  } { 1 "A" "A3"  } 
>>   { 0 "C" "C5"  } { 1 "C" "C3"  } 
>>   { 0 "U" "U5"  } { 1 "U" "U3"  } 
>>   { 0 "DG" "DG5"  } { 1 "DG" "DG3"  }  
>>   { 0 "DA" "DA5"  } { 1 "DA" "DA3"  }  
>>   { 0 "DC" "DC5"  } { 1 "DC" "DC3"  }  
>>   { 0 "DT" "DT5"  } { 1 "DT" "DT3"  }  
>> #  some old Amber residue names for RNA:
>>   { 0  "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" }
>>   { 0  "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" }
>>   { 0  "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" }
>>   { 0  "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" }
>> #  some really old Amber residue names, assuming DNA:
>>   { 0 "GUA" "DG5"  } { 1 "GUA" "DG3"  } { "GUA" "DG" }
>>   { 0 "ADE" "DA5"  } { 1 "ADE" "DA3"  } { "ADE" "DA" }
>>   { 0 "CYT" "DC5"  } { 1 "CYT" "DC3"  } { "CYT" "DC" }
>>   { 0 "THY" "DT5"  } { 1 "THY" "DT3"  } { "THY" "DT" }
>> #  uncomment out the following if you have this old style RNA files:
>> # { 0 "GUA" "G5"  } { 1 "GUA" "G3"  } { "GUA" "G" }
>> # { 0 "ADE" "A5"  } { 1 "ADE" "A3"  } { "ADE" "A" }
>> # { 0 "CYT" "C5"  } { 1 "CYT" "C3"  } { "CYT" "C" }
>> # { 0 "URA" "R5"  } { 1 "URA" "R3"  } { "URA" "R" }
>> 
>> }
>> 
>> #  try to be good about reading in really old atom names as well:
>> addPdbAtomMap {
>>   { "O5*" "O5'" }
>>   { "C5*" "C5'" }
>>   { "C4*" "C4'" }
>>   { "O4*" "O4'" }
>>   { "C3*" "C3'" }
>>   { "O3*" "O3'" }
>>   { "C2*" "C2'" }
>>   { "O2*" "O2'" }
>>   { "C1*" "C1'" }
>>   { "C5M" "C7"  }
>>   { "H1*" "H1'" }
>>   { "H2*1" "H2'" }
>>   { "H2*2" "H2''" }
>>   { "HO*2" "HO2'" }
>>   { "H2'1" "H2'" }
>>   { "H2'2" "H2''" }
>>   { "H3*" "H3'" }
>>   { "H4*" "H4'" }
>>   { "H5*1" "H5'" }
>>   { "H5*2" "H5''" }
>>   { "H5'1" "H5'" }
>>   { "H5'2" "H5''" }
>>   { "HO'2" "HO2'" }
>>   { "H5T"  "HO5'" }
>>   { "H3T"  "HO3'" }
>>   { "O1'" "O4'" }
>>   { "OA"  "OP1" }
>>   { "OB"  "OP2" }
>>   { "O1P" "OP1" }
>>   { "O2P" "OP2" }
>> }
>> 
>> #
>> # assume that most often proteins use HIE
>> #
>> NHIS = NHIE
>> HIS = HIE
>> CHIS = CHIE
> 
> loadoff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
> loadamberparams frcmod.opc
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.opc
Reading force field modification type file (frcmod)
Reading title:
Parameters for OPC water (JPCL, 2014, 5 (21), pp 3863–3871) 
(UNKNOWN ATOM TYPE: EP)
> loadamberparams frcmod.ionsjc_tip4pew
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip4pew
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP4P/EW water from Joung & Cheatham JPCB (2008)
> 
> m = loadpdb init.pdb
Loading PDB file: ./init.pdb
Enter zPdbReadScan from call depth  0.
Exit  zPdbReadScan from call depth  0.
Matching PDB residue names to LEaP variables.
(Residue 0: A5, Terminal/beginning, was not found in name map.)
(Residue 1: C3, Terminal/last, was not found in name map.)
Joining A5 - C3
  total atoms in file: 63
> 
> 
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.131155 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<H4' 9>
Warning: Close contact of 1.307451 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<C4' 8>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> solvatebox m OPCBOX 11 iso
  Solute vdw bounding box:              12.265 11.150 10.292
  Total bounding box for atom centers:  34.265 34.265 34.265
      (box expansion for 'iso' is   9.7%)
  Solvent unit box:                     18.865 18.478 19.006
The number of boxes:  x= 2  y= 2  z= 2
Adding box at: x=0  y=0  z=0
Center of solvent box is: 9.432422, 9.239054, 9.503120
Adding box at: x=0  y=0  z=1
Center of solvent box is: 9.432422, 9.239054, -9.503120
Adding box at: x=0  y=1  z=0
Center of solvent box is: 9.432422, -9.239054, 9.503120
Adding box at: x=0  y=1  z=1
Center of solvent box is: 9.432422, -9.239054, -9.503120
Adding box at: x=1  y=0  z=0
Center of solvent box is: -9.432422, 9.239054, 9.503120
Adding box at: x=1  y=0  z=1
Center of solvent box is: -9.432422, 9.239054, -9.503120
Adding box at: x=1  y=1  z=0
Center of solvent box is: -9.432422, -9.239054, 9.503120
Adding box at: x=1  y=1  z=1
Center of solvent box is: -9.432422, -9.239054, -9.503120
  Volume: 52632.886 A^3 
  Total mass 22118.568 amu,  Density 0.698 g/cc
  Added 1196 residues.
> quit
	Quit
log started: Sun Nov  1 20:52:16 2015

Log file: ./leap.log
>> #
>> # ----- leaprc for loading the ff12SB force field
>> # ----- NOTE: this is designed for PDB format 3!
>> #    Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA
>> #
>> #	load atom type hybridizations
>> #
>> addAtomTypes {
>> 	{ "H"   "H" "sp3" }
>> 	{ "HO"  "H" "sp3" }
>> 	{ "HS"  "H" "sp3" }
>> 	{ "H1"  "H" "sp3" }
>> 	{ "H2"  "H" "sp3" }
>> 	{ "H3"  "H" "sp3" }
>> 	{ "H4"  "H" "sp3" }
>> 	{ "H5"  "H" "sp3" }
>> 	{ "HW"  "H" "sp3" }
>> 	{ "HC"  "H" "sp3" }
>> 	{ "HA"  "H" "sp3" }
>> 	{ "HP"  "H" "sp3" }
>> 	{ "HZ"  "H" "sp3" }
>> 	{ "OH"  "O" "sp3" }
>> 	{ "OS"  "O" "sp3" }
>> 	{ "O"   "O" "sp2" }
>> 	{ "O2"  "O" "sp2" }
>> 	{ "OP"  "O" "sp2" }
>> 	{ "OW"  "O" "sp3" }
>> 	{ "CT"  "C" "sp3" }
>> 	{ "CX"  "C" "sp3" }
>> 	{ "C8"  "C" "sp3" }
>> 	{ "2C"  "C" "sp3" }
>> 	{ "3C"  "C" "sp3" }
>> 	{ "CH"  "C" "sp3" }
>> 	{ "CS"  "C" "sp2" }
>> 	{ "C"   "C" "sp2" }
>> 	{ "CO"   "C" "sp2" }
>> 	{ "C*"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CB"  "C" "sp2" }
>> 	{ "CC"  "C" "sp2" }
>> 	{ "CN"  "C" "sp2" }
>> 	{ "CM"  "C" "sp2" }
>> 	{ "CK"  "C" "sp2" }
>> 	{ "CQ"  "C" "sp2" }
>> 	{ "CD"  "C" "sp2" }
>> 	{ "C5"  "C" "sp2" }
>> 	{ "C4"  "C" "sp2" }
>> 	{ "CP"  "C" "sp2" }
>> 	{ "CI"  "C" "sp3" }
>> 	{ "CJ"  "C" "sp2" }
>> 	{ "CW"  "C" "sp2" }
>> 	{ "CV"  "C" "sp2" }
>> 	{ "CR"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CY"  "C" "sp2" }
>> 	{ "C0"  "Ca" "sp3" }
>> 	{ "MG"  "Mg" "sp3" }
>> 	{ "N"   "N" "sp2" }
>> 	{ "NA"  "N" "sp2" }
>> 	{ "N2"  "N" "sp2" }
>> 	{ "N*"  "N" "sp2" }
>> 	{ "NP"  "N" "sp2" }
>> 	{ "NQ"  "N" "sp2" }
>> 	{ "NB"  "N" "sp2" }
>> 	{ "NC"  "N" "sp2" }
>> 	{ "NT"  "N" "sp3" }
>> 	{ "NY"  "N" "sp2" }
>> 	{ "N3"  "N" "sp3" }
>> 	{ "S"   "S" "sp3" }
>> 	{ "SH"  "S" "sp3" }
>> 	{ "P"   "P" "sp3" }
>> 	{ "LP"  ""  "sp3" }
>> 	{ "EP"  ""  "sp3" }
>> 	{ "F"   "F" "sp3" }
>> 	{ "Cl"  "Cl" "sp3" }
>> 	{ "Br"  "Br" "sp3" }
>> 	{ "I"   "I"  "sp3" }
>> 	{ "F-"   "F" "sp3" }
>> 	{ "Cl-"  "Cl" "sp3" }
>> 	{ "Br-"  "Br" "sp3" }
>> 	{ "I-"   "I"  "sp3" }
>> 	{ "Li+"  "Li"  "sp3" }
>> 	{ "Na+"  "Na"  "sp3" }
>> 	{ "K+"  "K"  "sp3" }
>> 	{ "Rb+"  "Rb"  "sp3" }
>> 	{ "Cs+"  "Cs"  "sp3" }
>> 	{ "Mg+"  "Mg"  "sp3" }
>> # glycam
>> 	{ "OG"  "O" "sp3" }
>> 	{ "OL"  "O" "sp3" }
>> 	{ "AC"  "C" "sp3" }
>> 	{ "EC"  "C" "sp3" }
>> }
>> #
>> #	Load the main parameter set.
>> #
>> parm10 = loadamberparams parm10.dat
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
(UNKNOWN ATOM TYPE: Zn)
(UNKNOWN ATOM TYPE: EP)
>> frcmod12SB = loadamberparams frcmod.ff12SB
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff12SB
Reading force field modification type file (frcmod)
Reading title:
ff12SB protein backbone and sidechain parameters
>> #
>> #	Load main chain and terminating amino acid libraries, nucleic acids
>> #
>> loadOff amino12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/amino12.lib
Loading: ALA
Loading: ARG
Loading: ASH
Loading: ASN
Loading: ASP
Loading: CYM
Loading: CYS
Loading: CYX
Loading: GLH
Loading: GLN
Loading: GLU
Loading: GLY
Loading: HID
Loading: HIE
Loading: HIP
Loading: HYP
Loading: ILE
Loading: LEU
Loading: LYN
Loading: LYS
Loading: MET
Loading: PHE
Loading: PRO
Loading: SER
Loading: THR
Loading: TRP
Loading: TYR
Loading: VAL
>> loadOff aminoct12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminoct12.lib
Loading: CALA
Loading: CARG
Loading: CASN
Loading: CASP
Loading: CCYS
Loading: CCYX
Loading: CGLN
Loading: CGLU
Loading: CGLY
Loading: CHID
Loading: CHIE
Loading: CHIP
Loading: CHYP
Loading: CILE
Loading: CLEU
Loading: CLYS
Loading: CMET
Loading: CPHE
Loading: CPRO
Loading: CSER
Loading: CTHR
Loading: CTRP
Loading: CTYR
Loading: CVAL
Loading: NHE
Loading: NME
>> loadOff aminont12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminont12.lib
Loading: ACE
Loading: NALA
Loading: NARG
Loading: NASN
Loading: NASP
Loading: NCYS
Loading: NCYX
Loading: NGLN
Loading: NGLU
Loading: NGLY
Loading: NHID
Loading: NHIE
Loading: NHIP
Loading: NILE
Loading: NLEU
Loading: NLYS
Loading: NMET
Loading: NPHE
Loading: NPRO
Loading: NSER
Loading: NTHR
Loading: NTRP
Loading: NTYR
Loading: NVAL
>> loadOff nucleic12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/nucleic12.lib
Loading: A
Loading: A3
Loading: A5
Loading: AN
Loading: C
Loading: C3
Loading: C5
Loading: CN
Loading: DA
Loading: DA3
Loading: DA5
Loading: DAN
Loading: DC
Loading: DC3
Loading: DC5
Loading: DCN
Loading: DG
Loading: DG3
Loading: DG5
Loading: DGN
Loading: DT
Loading: DT3
Loading: DT5
Loading: DTN
Loading: G
Loading: G3
Loading: G5
Loading: GN
Loading: OHE
Loading: U
Loading: U3
Loading: U5
Loading: UN
>> #
>> #       Load water and ions
>> # 
>> loadOff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
>> loadOff solvents.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: MEOHBOX
Loading: NMABOX
Loading: OPC
Loading: OPCBOX
Loading: PL3
Loading: POL3BOX
Loading: QSPCFWBOX
Loading: SPC
Loading: SPCBOX
Loading: SPCFWBOX
Loading: SPF
Loading: SPG
Loading: T4E
Loading: TIP3PBOX
Loading: TIP3PFBOX
Loading: TIP4PBOX
Loading: TIP4PEWBOX
Loading: TIP5PBOX
Loading: TP3
Loading: TP4
Loading: TP5
Loading: TPF
>> HOH = TP3
>> WAT = TP3
>> 
>> #
>> #	Define the PDB name map for the amino acids and nucleic acids
>> #     (note: no NHYP!  use neutral form for now)
>> #
>> addPdbResMap {
>>   { 0 "HYP" "HYP"  } { 1 "HYP" "CHYP" }
>>   { 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
>>   { 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
>>   { 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
>>   { 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
>>   { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
>>   { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
>>   { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
>>   { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
>>   { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
>>   { 0 "HID" "NHID" } { 1 "HID" "CHID" }
>>   { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
>>   { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
>>   { 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
>>   { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
>>   { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
>>   { 0 "MET" "NMET" } { 1 "MET" "CMET" }
>>   { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
>>   { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
>>   { 0 "SER" "NSER" } { 1 "SER" "CSER" }
>>   { 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
>>   { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
>>   { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
>>   { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
>>   { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
>>   { 0 "G" "G5"  } { 1 "G" "G3"  } 
>>   { 0 "A" "A5"  } { 1 "A" "A3"  } 
>>   { 0 "C" "C5"  } { 1 "C" "C3"  } 
>>   { 0 "U" "U5"  } { 1 "U" "U3"  } 
>>   { 0 "DG" "DG5"  } { 1 "DG" "DG3"  }  
>>   { 0 "DA" "DA5"  } { 1 "DA" "DA3"  }  
>>   { 0 "DC" "DC5"  } { 1 "DC" "DC3"  }  
>>   { 0 "DT" "DT5"  } { 1 "DT" "DT3"  }  
>> #  some old Amber residue names for RNA:
>>   { 0  "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" }
>>   { 0  "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" }
>>   { 0  "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" }
>>   { 0  "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" }
>> #  some really old Amber residue names, assuming DNA:
>>   { 0 "GUA" "DG5"  } { 1 "GUA" "DG3"  } { "GUA" "DG" }
>>   { 0 "ADE" "DA5"  } { 1 "ADE" "DA3"  } { "ADE" "DA" }
>>   { 0 "CYT" "DC5"  } { 1 "CYT" "DC3"  } { "CYT" "DC" }
>>   { 0 "THY" "DT5"  } { 1 "THY" "DT3"  } { "THY" "DT" }
>> #  uncomment out the following if you have this old style RNA files:
>> # { 0 "GUA" "G5"  } { 1 "GUA" "G3"  } { "GUA" "G" }
>> # { 0 "ADE" "A5"  } { 1 "ADE" "A3"  } { "ADE" "A" }
>> # { 0 "CYT" "C5"  } { 1 "CYT" "C3"  } { "CYT" "C" }
>> # { 0 "URA" "R5"  } { 1 "URA" "R3"  } { "URA" "R" }
>> 
>> }
>> 
>> #  try to be good about reading in really old atom names as well:
>> addPdbAtomMap {
>>   { "O5*" "O5'" }
>>   { "C5*" "C5'" }
>>   { "C4*" "C4'" }
>>   { "O4*" "O4'" }
>>   { "C3*" "C3'" }
>>   { "O3*" "O3'" }
>>   { "C2*" "C2'" }
>>   { "O2*" "O2'" }
>>   { "C1*" "C1'" }
>>   { "C5M" "C7"  }
>>   { "H1*" "H1'" }
>>   { "H2*1" "H2'" }
>>   { "H2*2" "H2''" }
>>   { "HO*2" "HO2'" }
>>   { "H2'1" "H2'" }
>>   { "H2'2" "H2''" }
>>   { "H3*" "H3'" }
>>   { "H4*" "H4'" }
>>   { "H5*1" "H5'" }
>>   { "H5*2" "H5''" }
>>   { "H5'1" "H5'" }
>>   { "H5'2" "H5''" }
>>   { "HO'2" "HO2'" }
>>   { "H5T"  "HO5'" }
>>   { "H3T"  "HO3'" }
>>   { "O1'" "O4'" }
>>   { "OA"  "OP1" }
>>   { "OB"  "OP2" }
>>   { "O1P" "OP1" }
>>   { "O2P" "OP2" }
>> }
>> 
>> #
>> # assume that most often proteins use HIE
>> #
>> NHIS = NHIE
>> HIS = HIE
>> CHIS = CHIE
> 
> loadoff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
> loadamberparams frcmod.opc
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.opc
Reading force field modification type file (frcmod)
Reading title:
Parameters for OPC water (JPCL, 2014, 5 (21), pp 3863–3871) 
(UNKNOWN ATOM TYPE: EP)
> loadamberparams frcmod.ionsjc_tip4pew
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip4pew
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP4P/EW water from Joung & Cheatham JPCB (2008)
> 
> m = loadpdb init.pdb
Loading PDB file: ./init.pdb
Enter zPdbReadScan from call depth  0.
Exit  zPdbReadScan from call depth  0.
Matching PDB residue names to LEaP variables.
(Residue 0: A5, Terminal/beginning, was not found in name map.)
(Residue 1: C3, Terminal/last, was not found in name map.)
Joining A5 - C3
  total atoms in file: 63
> 
> 
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.131155 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<H4' 9>
Warning: Close contact of 1.307451 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<C4' 8>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> solvatebox m OPCBOX 10.5 iso
  Solute vdw bounding box:              12.265 11.150 10.292
  Total bounding box for atom centers:  33.265 33.265 33.265
      (box expansion for 'iso' is  10.0%)
  Solvent unit box:                     18.865 18.478 19.006
The number of boxes:  x= 2  y= 2  z= 2
Adding box at: x=0  y=0  z=0
Center of solvent box is: 9.432422, 9.239054, 9.503120
Adding box at: x=0  y=0  z=1
Center of solvent box is: 9.432422, 9.239054, -9.503120
Adding box at: x=0  y=1  z=0
Center of solvent box is: 9.432422, -9.239054, 9.503120
Adding box at: x=0  y=1  z=1
Center of solvent box is: 9.432422, -9.239054, -9.503120
Adding box at: x=1  y=0  z=0
Center of solvent box is: -9.432422, 9.239054, 9.503120
Adding box at: x=1  y=0  z=1
Center of solvent box is: -9.432422, 9.239054, -9.503120
Adding box at: x=1  y=1  z=0
Center of solvent box is: -9.432422, -9.239054, 9.503120
Adding box at: x=1  y=1  z=1
Center of solvent box is: -9.432422, -9.239054, -9.503120
  Volume: 47132.626 A^3 
  Total mass 19506.248 amu,  Density 0.687 g/cc
  Added 1051 residues.
> quit
	Quit
log started: Sun Nov  1 20:52:16 2015

Log file: ./leap.log
>> #
>> # ----- leaprc for loading the ff12SB force field
>> # ----- NOTE: this is designed for PDB format 3!
>> #    Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA
>> #
>> #	load atom type hybridizations
>> #
>> addAtomTypes {
>> 	{ "H"   "H" "sp3" }
>> 	{ "HO"  "H" "sp3" }
>> 	{ "HS"  "H" "sp3" }
>> 	{ "H1"  "H" "sp3" }
>> 	{ "H2"  "H" "sp3" }
>> 	{ "H3"  "H" "sp3" }
>> 	{ "H4"  "H" "sp3" }
>> 	{ "H5"  "H" "sp3" }
>> 	{ "HW"  "H" "sp3" }
>> 	{ "HC"  "H" "sp3" }
>> 	{ "HA"  "H" "sp3" }
>> 	{ "HP"  "H" "sp3" }
>> 	{ "HZ"  "H" "sp3" }
>> 	{ "OH"  "O" "sp3" }
>> 	{ "OS"  "O" "sp3" }
>> 	{ "O"   "O" "sp2" }
>> 	{ "O2"  "O" "sp2" }
>> 	{ "OP"  "O" "sp2" }
>> 	{ "OW"  "O" "sp3" }
>> 	{ "CT"  "C" "sp3" }
>> 	{ "CX"  "C" "sp3" }
>> 	{ "C8"  "C" "sp3" }
>> 	{ "2C"  "C" "sp3" }
>> 	{ "3C"  "C" "sp3" }
>> 	{ "CH"  "C" "sp3" }
>> 	{ "CS"  "C" "sp2" }
>> 	{ "C"   "C" "sp2" }
>> 	{ "CO"   "C" "sp2" }
>> 	{ "C*"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CB"  "C" "sp2" }
>> 	{ "CC"  "C" "sp2" }
>> 	{ "CN"  "C" "sp2" }
>> 	{ "CM"  "C" "sp2" }
>> 	{ "CK"  "C" "sp2" }
>> 	{ "CQ"  "C" "sp2" }
>> 	{ "CD"  "C" "sp2" }
>> 	{ "C5"  "C" "sp2" }
>> 	{ "C4"  "C" "sp2" }
>> 	{ "CP"  "C" "sp2" }
>> 	{ "CI"  "C" "sp3" }
>> 	{ "CJ"  "C" "sp2" }
>> 	{ "CW"  "C" "sp2" }
>> 	{ "CV"  "C" "sp2" }
>> 	{ "CR"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CY"  "C" "sp2" }
>> 	{ "C0"  "Ca" "sp3" }
>> 	{ "MG"  "Mg" "sp3" }
>> 	{ "N"   "N" "sp2" }
>> 	{ "NA"  "N" "sp2" }
>> 	{ "N2"  "N" "sp2" }
>> 	{ "N*"  "N" "sp2" }
>> 	{ "NP"  "N" "sp2" }
>> 	{ "NQ"  "N" "sp2" }
>> 	{ "NB"  "N" "sp2" }
>> 	{ "NC"  "N" "sp2" }
>> 	{ "NT"  "N" "sp3" }
>> 	{ "NY"  "N" "sp2" }
>> 	{ "N3"  "N" "sp3" }
>> 	{ "S"   "S" "sp3" }
>> 	{ "SH"  "S" "sp3" }
>> 	{ "P"   "P" "sp3" }
>> 	{ "LP"  ""  "sp3" }
>> 	{ "EP"  ""  "sp3" }
>> 	{ "F"   "F" "sp3" }
>> 	{ "Cl"  "Cl" "sp3" }
>> 	{ "Br"  "Br" "sp3" }
>> 	{ "I"   "I"  "sp3" }
>> 	{ "F-"   "F" "sp3" }
>> 	{ "Cl-"  "Cl" "sp3" }
>> 	{ "Br-"  "Br" "sp3" }
>> 	{ "I-"   "I"  "sp3" }
>> 	{ "Li+"  "Li"  "sp3" }
>> 	{ "Na+"  "Na"  "sp3" }
>> 	{ "K+"  "K"  "sp3" }
>> 	{ "Rb+"  "Rb"  "sp3" }
>> 	{ "Cs+"  "Cs"  "sp3" }
>> 	{ "Mg+"  "Mg"  "sp3" }
>> # glycam
>> 	{ "OG"  "O" "sp3" }
>> 	{ "OL"  "O" "sp3" }
>> 	{ "AC"  "C" "sp3" }
>> 	{ "EC"  "C" "sp3" }
>> }
>> #
>> #	Load the main parameter set.
>> #
>> parm10 = loadamberparams parm10.dat
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
(UNKNOWN ATOM TYPE: Zn)
(UNKNOWN ATOM TYPE: EP)
>> frcmod12SB = loadamberparams frcmod.ff12SB
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff12SB
Reading force field modification type file (frcmod)
Reading title:
ff12SB protein backbone and sidechain parameters
>> #
>> #	Load main chain and terminating amino acid libraries, nucleic acids
>> #
>> loadOff amino12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/amino12.lib
Loading: ALA
Loading: ARG
Loading: ASH
Loading: ASN
Loading: ASP
Loading: CYM
Loading: CYS
Loading: CYX
Loading: GLH
Loading: GLN
Loading: GLU
Loading: GLY
Loading: HID
Loading: HIE
Loading: HIP
Loading: HYP
Loading: ILE
Loading: LEU
Loading: LYN
Loading: LYS
Loading: MET
Loading: PHE
Loading: PRO
Loading: SER
Loading: THR
Loading: TRP
Loading: TYR
Loading: VAL
>> loadOff aminoct12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminoct12.lib
Loading: CALA
Loading: CARG
Loading: CASN
Loading: CASP
Loading: CCYS
Loading: CCYX
Loading: CGLN
Loading: CGLU
Loading: CGLY
Loading: CHID
Loading: CHIE
Loading: CHIP
Loading: CHYP
Loading: CILE
Loading: CLEU
Loading: CLYS
Loading: CMET
Loading: CPHE
Loading: CPRO
Loading: CSER
Loading: CTHR
Loading: CTRP
Loading: CTYR
Loading: CVAL
Loading: NHE
Loading: NME
>> loadOff aminont12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminont12.lib
Loading: ACE
Loading: NALA
Loading: NARG
Loading: NASN
Loading: NASP
Loading: NCYS
Loading: NCYX
Loading: NGLN
Loading: NGLU
Loading: NGLY
Loading: NHID
Loading: NHIE
Loading: NHIP
Loading: NILE
Loading: NLEU
Loading: NLYS
Loading: NMET
Loading: NPHE
Loading: NPRO
Loading: NSER
Loading: NTHR
Loading: NTRP
Loading: NTYR
Loading: NVAL
>> loadOff nucleic12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/nucleic12.lib
Loading: A
Loading: A3
Loading: A5
Loading: AN
Loading: C
Loading: C3
Loading: C5
Loading: CN
Loading: DA
Loading: DA3
Loading: DA5
Loading: DAN
Loading: DC
Loading: DC3
Loading: DC5
Loading: DCN
Loading: DG
Loading: DG3
Loading: DG5
Loading: DGN
Loading: DT
Loading: DT3
Loading: DT5
Loading: DTN
Loading: G
Loading: G3
Loading: G5
Loading: GN
Loading: OHE
Loading: U
Loading: U3
Loading: U5
Loading: UN
>> #
>> #       Load water and ions
>> # 
>> loadOff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
>> loadOff solvents.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: MEOHBOX
Loading: NMABOX
Loading: OPC
Loading: OPCBOX
Loading: PL3
Loading: POL3BOX
Loading: QSPCFWBOX
Loading: SPC
Loading: SPCBOX
Loading: SPCFWBOX
Loading: SPF
Loading: SPG
Loading: T4E
Loading: TIP3PBOX
Loading: TIP3PFBOX
Loading: TIP4PBOX
Loading: TIP4PEWBOX
Loading: TIP5PBOX
Loading: TP3
Loading: TP4
Loading: TP5
Loading: TPF
>> HOH = TP3
>> WAT = TP3
>> 
>> #
>> #	Define the PDB name map for the amino acids and nucleic acids
>> #     (note: no NHYP!  use neutral form for now)
>> #
>> addPdbResMap {
>>   { 0 "HYP" "HYP"  } { 1 "HYP" "CHYP" }
>>   { 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
>>   { 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
>>   { 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
>>   { 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
>>   { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
>>   { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
>>   { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
>>   { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
>>   { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
>>   { 0 "HID" "NHID" } { 1 "HID" "CHID" }
>>   { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
>>   { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
>>   { 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
>>   { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
>>   { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
>>   { 0 "MET" "NMET" } { 1 "MET" "CMET" }
>>   { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
>>   { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
>>   { 0 "SER" "NSER" } { 1 "SER" "CSER" }
>>   { 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
>>   { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
>>   { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
>>   { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
>>   { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
>>   { 0 "G" "G5"  } { 1 "G" "G3"  } 
>>   { 0 "A" "A5"  } { 1 "A" "A3"  } 
>>   { 0 "C" "C5"  } { 1 "C" "C3"  } 
>>   { 0 "U" "U5"  } { 1 "U" "U3"  } 
>>   { 0 "DG" "DG5"  } { 1 "DG" "DG3"  }  
>>   { 0 "DA" "DA5"  } { 1 "DA" "DA3"  }  
>>   { 0 "DC" "DC5"  } { 1 "DC" "DC3"  }  
>>   { 0 "DT" "DT5"  } { 1 "DT" "DT3"  }  
>> #  some old Amber residue names for RNA:
>>   { 0  "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" }
>>   { 0  "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" }
>>   { 0  "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" }
>>   { 0  "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" }
>> #  some really old Amber residue names, assuming DNA:
>>   { 0 "GUA" "DG5"  } { 1 "GUA" "DG3"  } { "GUA" "DG" }
>>   { 0 "ADE" "DA5"  } { 1 "ADE" "DA3"  } { "ADE" "DA" }
>>   { 0 "CYT" "DC5"  } { 1 "CYT" "DC3"  } { "CYT" "DC" }
>>   { 0 "THY" "DT5"  } { 1 "THY" "DT3"  } { "THY" "DT" }
>> #  uncomment out the following if you have this old style RNA files:
>> # { 0 "GUA" "G5"  } { 1 "GUA" "G3"  } { "GUA" "G" }
>> # { 0 "ADE" "A5"  } { 1 "ADE" "A3"  } { "ADE" "A" }
>> # { 0 "CYT" "C5"  } { 1 "CYT" "C3"  } { "CYT" "C" }
>> # { 0 "URA" "R5"  } { 1 "URA" "R3"  } { "URA" "R" }
>> 
>> }
>> 
>> #  try to be good about reading in really old atom names as well:
>> addPdbAtomMap {
>>   { "O5*" "O5'" }
>>   { "C5*" "C5'" }
>>   { "C4*" "C4'" }
>>   { "O4*" "O4'" }
>>   { "C3*" "C3'" }
>>   { "O3*" "O3'" }
>>   { "C2*" "C2'" }
>>   { "O2*" "O2'" }
>>   { "C1*" "C1'" }
>>   { "C5M" "C7"  }
>>   { "H1*" "H1'" }
>>   { "H2*1" "H2'" }
>>   { "H2*2" "H2''" }
>>   { "HO*2" "HO2'" }
>>   { "H2'1" "H2'" }
>>   { "H2'2" "H2''" }
>>   { "H3*" "H3'" }
>>   { "H4*" "H4'" }
>>   { "H5*1" "H5'" }
>>   { "H5*2" "H5''" }
>>   { "H5'1" "H5'" }
>>   { "H5'2" "H5''" }
>>   { "HO'2" "HO2'" }
>>   { "H5T"  "HO5'" }
>>   { "H3T"  "HO3'" }
>>   { "O1'" "O4'" }
>>   { "OA"  "OP1" }
>>   { "OB"  "OP2" }
>>   { "O1P" "OP1" }
>>   { "O2P" "OP2" }
>> }
>> 
>> #
>> # assume that most often proteins use HIE
>> #
>> NHIS = NHIE
>> HIS = HIE
>> CHIS = CHIE
> 
> loadoff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
> loadamberparams frcmod.opc
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.opc
Reading force field modification type file (frcmod)
Reading title:
Parameters for OPC water (JPCL, 2014, 5 (21), pp 3863–3871) 
(UNKNOWN ATOM TYPE: EP)
> loadamberparams frcmod.ionsjc_tip4pew
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip4pew
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP4P/EW water from Joung & Cheatham JPCB (2008)
> 
> m = loadpdb init.pdb
Loading PDB file: ./init.pdb
Enter zPdbReadScan from call depth  0.
Exit  zPdbReadScan from call depth  0.
Matching PDB residue names to LEaP variables.
(Residue 0: A5, Terminal/beginning, was not found in name map.)
(Residue 1: C3, Terminal/last, was not found in name map.)
Joining A5 - C3
  total atoms in file: 63
> 
> 
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.131155 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<H4' 9>
Warning: Close contact of 1.307451 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<C4' 8>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> solvatebox m OPCBOX 10.6 iso
  Solute vdw bounding box:              12.265 11.150 10.292
  Total bounding box for atom centers:  33.465 33.465 33.465
      (box expansion for 'iso' is   9.9%)
  Solvent unit box:                     18.865 18.478 19.006
The number of boxes:  x= 2  y= 2  z= 2
Adding box at: x=0  y=0  z=0
Center of solvent box is: 9.432422, 9.239054, 9.503120
Adding box at: x=0  y=0  z=1
Center of solvent box is: 9.432422, 9.239054, -9.503120
Adding box at: x=0  y=1  z=0
Center of solvent box is: 9.432422, -9.239054, 9.503120
Adding box at: x=0  y=1  z=1
Center of solvent box is: 9.432422, -9.239054, -9.503120
Adding box at: x=1  y=0  z=0
Center of solvent box is: -9.432422, 9.239054, 9.503120
Adding box at: x=1  y=0  z=1
Center of solvent box is: -9.432422, 9.239054, -9.503120
Adding box at: x=1  y=1  z=0
Center of solvent box is: -9.432422, -9.239054, 9.503120
Adding box at: x=1  y=1  z=1
Center of solvent box is: -9.432422, -9.239054, -9.503120
  Volume: 47135.242 A^3 
  Total mass 19830.536 amu,  Density 0.699 g/cc
  Added 1069 residues.
> quit
	Quit
log started: Sun Nov  1 20:52:16 2015

Log file: ./leap.log
>> #
>> # ----- leaprc for loading the ff12SB force field
>> # ----- NOTE: this is designed for PDB format 3!
>> #    Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA
>> #
>> #	load atom type hybridizations
>> #
>> addAtomTypes {
>> 	{ "H"   "H" "sp3" }
>> 	{ "HO"  "H" "sp3" }
>> 	{ "HS"  "H" "sp3" }
>> 	{ "H1"  "H" "sp3" }
>> 	{ "H2"  "H" "sp3" }
>> 	{ "H3"  "H" "sp3" }
>> 	{ "H4"  "H" "sp3" }
>> 	{ "H5"  "H" "sp3" }
>> 	{ "HW"  "H" "sp3" }
>> 	{ "HC"  "H" "sp3" }
>> 	{ "HA"  "H" "sp3" }
>> 	{ "HP"  "H" "sp3" }
>> 	{ "HZ"  "H" "sp3" }
>> 	{ "OH"  "O" "sp3" }
>> 	{ "OS"  "O" "sp3" }
>> 	{ "O"   "O" "sp2" }
>> 	{ "O2"  "O" "sp2" }
>> 	{ "OP"  "O" "sp2" }
>> 	{ "OW"  "O" "sp3" }
>> 	{ "CT"  "C" "sp3" }
>> 	{ "CX"  "C" "sp3" }
>> 	{ "C8"  "C" "sp3" }
>> 	{ "2C"  "C" "sp3" }
>> 	{ "3C"  "C" "sp3" }
>> 	{ "CH"  "C" "sp3" }
>> 	{ "CS"  "C" "sp2" }
>> 	{ "C"   "C" "sp2" }
>> 	{ "CO"   "C" "sp2" }
>> 	{ "C*"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CB"  "C" "sp2" }
>> 	{ "CC"  "C" "sp2" }
>> 	{ "CN"  "C" "sp2" }
>> 	{ "CM"  "C" "sp2" }
>> 	{ "CK"  "C" "sp2" }
>> 	{ "CQ"  "C" "sp2" }
>> 	{ "CD"  "C" "sp2" }
>> 	{ "C5"  "C" "sp2" }
>> 	{ "C4"  "C" "sp2" }
>> 	{ "CP"  "C" "sp2" }
>> 	{ "CI"  "C" "sp3" }
>> 	{ "CJ"  "C" "sp2" }
>> 	{ "CW"  "C" "sp2" }
>> 	{ "CV"  "C" "sp2" }
>> 	{ "CR"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CY"  "C" "sp2" }
>> 	{ "C0"  "Ca" "sp3" }
>> 	{ "MG"  "Mg" "sp3" }
>> 	{ "N"   "N" "sp2" }
>> 	{ "NA"  "N" "sp2" }
>> 	{ "N2"  "N" "sp2" }
>> 	{ "N*"  "N" "sp2" }
>> 	{ "NP"  "N" "sp2" }
>> 	{ "NQ"  "N" "sp2" }
>> 	{ "NB"  "N" "sp2" }
>> 	{ "NC"  "N" "sp2" }
>> 	{ "NT"  "N" "sp3" }
>> 	{ "NY"  "N" "sp2" }
>> 	{ "N3"  "N" "sp3" }
>> 	{ "S"   "S" "sp3" }
>> 	{ "SH"  "S" "sp3" }
>> 	{ "P"   "P" "sp3" }
>> 	{ "LP"  ""  "sp3" }
>> 	{ "EP"  ""  "sp3" }
>> 	{ "F"   "F" "sp3" }
>> 	{ "Cl"  "Cl" "sp3" }
>> 	{ "Br"  "Br" "sp3" }
>> 	{ "I"   "I"  "sp3" }
>> 	{ "F-"   "F" "sp3" }
>> 	{ "Cl-"  "Cl" "sp3" }
>> 	{ "Br-"  "Br" "sp3" }
>> 	{ "I-"   "I"  "sp3" }
>> 	{ "Li+"  "Li"  "sp3" }
>> 	{ "Na+"  "Na"  "sp3" }
>> 	{ "K+"  "K"  "sp3" }
>> 	{ "Rb+"  "Rb"  "sp3" }
>> 	{ "Cs+"  "Cs"  "sp3" }
>> 	{ "Mg+"  "Mg"  "sp3" }
>> # glycam
>> 	{ "OG"  "O" "sp3" }
>> 	{ "OL"  "O" "sp3" }
>> 	{ "AC"  "C" "sp3" }
>> 	{ "EC"  "C" "sp3" }
>> }
>> #
>> #	Load the main parameter set.
>> #
>> parm10 = loadamberparams parm10.dat
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
(UNKNOWN ATOM TYPE: Zn)
(UNKNOWN ATOM TYPE: EP)
>> frcmod12SB = loadamberparams frcmod.ff12SB
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff12SB
Reading force field modification type file (frcmod)
Reading title:
ff12SB protein backbone and sidechain parameters
>> #
>> #	Load main chain and terminating amino acid libraries, nucleic acids
>> #
>> loadOff amino12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/amino12.lib
Loading: ALA
Loading: ARG
Loading: ASH
Loading: ASN
Loading: ASP
Loading: CYM
Loading: CYS
Loading: CYX
Loading: GLH
Loading: GLN
Loading: GLU
Loading: GLY
Loading: HID
Loading: HIE
Loading: HIP
Loading: HYP
Loading: ILE
Loading: LEU
Loading: LYN
Loading: LYS
Loading: MET
Loading: PHE
Loading: PRO
Loading: SER
Loading: THR
Loading: TRP
Loading: TYR
Loading: VAL
>> loadOff aminoct12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminoct12.lib
Loading: CALA
Loading: CARG
Loading: CASN
Loading: CASP
Loading: CCYS
Loading: CCYX
Loading: CGLN
Loading: CGLU
Loading: CGLY
Loading: CHID
Loading: CHIE
Loading: CHIP
Loading: CHYP
Loading: CILE
Loading: CLEU
Loading: CLYS
Loading: CMET
Loading: CPHE
Loading: CPRO
Loading: CSER
Loading: CTHR
Loading: CTRP
Loading: CTYR
Loading: CVAL
Loading: NHE
Loading: NME
>> loadOff aminont12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminont12.lib
Loading: ACE
Loading: NALA
Loading: NARG
Loading: NASN
Loading: NASP
Loading: NCYS
Loading: NCYX
Loading: NGLN
Loading: NGLU
Loading: NGLY
Loading: NHID
Loading: NHIE
Loading: NHIP
Loading: NILE
Loading: NLEU
Loading: NLYS
Loading: NMET
Loading: NPHE
Loading: NPRO
Loading: NSER
Loading: NTHR
Loading: NTRP
Loading: NTYR
Loading: NVAL
>> loadOff nucleic12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/nucleic12.lib
Loading: A
Loading: A3
Loading: A5
Loading: AN
Loading: C
Loading: C3
Loading: C5
Loading: CN
Loading: DA
Loading: DA3
Loading: DA5
Loading: DAN
Loading: DC
Loading: DC3
Loading: DC5
Loading: DCN
Loading: DG
Loading: DG3
Loading: DG5
Loading: DGN
Loading: DT
Loading: DT3
Loading: DT5
Loading: DTN
Loading: G
Loading: G3
Loading: G5
Loading: GN
Loading: OHE
Loading: U
Loading: U3
Loading: U5
Loading: UN
>> #
>> #       Load water and ions
>> # 
>> loadOff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
>> loadOff solvents.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: MEOHBOX
Loading: NMABOX
Loading: OPC
Loading: OPCBOX
Loading: PL3
Loading: POL3BOX
Loading: QSPCFWBOX
Loading: SPC
Loading: SPCBOX
Loading: SPCFWBOX
Loading: SPF
Loading: SPG
Loading: T4E
Loading: TIP3PBOX
Loading: TIP3PFBOX
Loading: TIP4PBOX
Loading: TIP4PEWBOX
Loading: TIP5PBOX
Loading: TP3
Loading: TP4
Loading: TP5
Loading: TPF
>> HOH = TP3
>> WAT = TP3
>> 
>> #
>> #	Define the PDB name map for the amino acids and nucleic acids
>> #     (note: no NHYP!  use neutral form for now)
>> #
>> addPdbResMap {
>>   { 0 "HYP" "HYP"  } { 1 "HYP" "CHYP" }
>>   { 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
>>   { 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
>>   { 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
>>   { 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
>>   { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
>>   { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
>>   { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
>>   { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
>>   { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
>>   { 0 "HID" "NHID" } { 1 "HID" "CHID" }
>>   { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
>>   { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
>>   { 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
>>   { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
>>   { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
>>   { 0 "MET" "NMET" } { 1 "MET" "CMET" }
>>   { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
>>   { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
>>   { 0 "SER" "NSER" } { 1 "SER" "CSER" }
>>   { 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
>>   { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
>>   { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
>>   { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
>>   { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
>>   { 0 "G" "G5"  } { 1 "G" "G3"  } 
>>   { 0 "A" "A5"  } { 1 "A" "A3"  } 
>>   { 0 "C" "C5"  } { 1 "C" "C3"  } 
>>   { 0 "U" "U5"  } { 1 "U" "U3"  } 
>>   { 0 "DG" "DG5"  } { 1 "DG" "DG3"  }  
>>   { 0 "DA" "DA5"  } { 1 "DA" "DA3"  }  
>>   { 0 "DC" "DC5"  } { 1 "DC" "DC3"  }  
>>   { 0 "DT" "DT5"  } { 1 "DT" "DT3"  }  
>> #  some old Amber residue names for RNA:
>>   { 0  "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" }
>>   { 0  "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" }
>>   { 0  "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" }
>>   { 0  "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" }
>> #  some really old Amber residue names, assuming DNA:
>>   { 0 "GUA" "DG5"  } { 1 "GUA" "DG3"  } { "GUA" "DG" }
>>   { 0 "ADE" "DA5"  } { 1 "ADE" "DA3"  } { "ADE" "DA" }
>>   { 0 "CYT" "DC5"  } { 1 "CYT" "DC3"  } { "CYT" "DC" }
>>   { 0 "THY" "DT5"  } { 1 "THY" "DT3"  } { "THY" "DT" }
>> #  uncomment out the following if you have this old style RNA files:
>> # { 0 "GUA" "G5"  } { 1 "GUA" "G3"  } { "GUA" "G" }
>> # { 0 "ADE" "A5"  } { 1 "ADE" "A3"  } { "ADE" "A" }
>> # { 0 "CYT" "C5"  } { 1 "CYT" "C3"  } { "CYT" "C" }
>> # { 0 "URA" "R5"  } { 1 "URA" "R3"  } { "URA" "R" }
>> 
>> }
>> 
>> #  try to be good about reading in really old atom names as well:
>> addPdbAtomMap {
>>   { "O5*" "O5'" }
>>   { "C5*" "C5'" }
>>   { "C4*" "C4'" }
>>   { "O4*" "O4'" }
>>   { "C3*" "C3'" }
>>   { "O3*" "O3'" }
>>   { "C2*" "C2'" }
>>   { "O2*" "O2'" }
>>   { "C1*" "C1'" }
>>   { "C5M" "C7"  }
>>   { "H1*" "H1'" }
>>   { "H2*1" "H2'" }
>>   { "H2*2" "H2''" }
>>   { "HO*2" "HO2'" }
>>   { "H2'1" "H2'" }
>>   { "H2'2" "H2''" }
>>   { "H3*" "H3'" }
>>   { "H4*" "H4'" }
>>   { "H5*1" "H5'" }
>>   { "H5*2" "H5''" }
>>   { "H5'1" "H5'" }
>>   { "H5'2" "H5''" }
>>   { "HO'2" "HO2'" }
>>   { "H5T"  "HO5'" }
>>   { "H3T"  "HO3'" }
>>   { "O1'" "O4'" }
>>   { "OA"  "OP1" }
>>   { "OB"  "OP2" }
>>   { "O1P" "OP1" }
>>   { "O2P" "OP2" }
>> }
>> 
>> #
>> # assume that most often proteins use HIE
>> #
>> NHIS = NHIE
>> HIS = HIE
>> CHIS = CHIE
> 
> loadoff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
> loadamberparams frcmod.opc
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.opc
Reading force field modification type file (frcmod)
Reading title:
Parameters for OPC water (JPCL, 2014, 5 (21), pp 3863–3871) 
(UNKNOWN ATOM TYPE: EP)
> loadamberparams frcmod.ionsjc_tip4pew
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip4pew
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP4P/EW water from Joung & Cheatham JPCB (2008)
> 
> m = loadpdb init.pdb
Loading PDB file: ./init.pdb
Enter zPdbReadScan from call depth  0.
Exit  zPdbReadScan from call depth  0.
Matching PDB residue names to LEaP variables.
(Residue 0: A5, Terminal/beginning, was not found in name map.)
(Residue 1: C3, Terminal/last, was not found in name map.)
Joining A5 - C3
  total atoms in file: 63
> 
> 
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.131155 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<H4' 9>
Warning: Close contact of 1.307451 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<C4' 8>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> solvatebox m OPCBOX 10.7 iso
  Solute vdw bounding box:              12.265 11.150 10.292
  Total bounding box for atom centers:  33.665 33.665 33.665
      (box expansion for 'iso' is   9.9%)
  Solvent unit box:                     18.865 18.478 19.006
The number of boxes:  x= 2  y= 2  z= 2
Adding box at: x=0  y=0  z=0
Center of solvent box is: 9.432422, 9.239054, 9.503120
Adding box at: x=0  y=0  z=1
Center of solvent box is: 9.432422, 9.239054, -9.503120
Adding box at: x=0  y=1  z=0
Center of solvent box is: 9.432422, -9.239054, 9.503120
Adding box at: x=0  y=1  z=1
Center of solvent box is: 9.432422, -9.239054, -9.503120
Adding box at: x=1  y=0  z=0
Center of solvent box is: -9.432422, 9.239054, 9.503120
Adding box at: x=1  y=0  z=1
Center of solvent box is: -9.432422, 9.239054, -9.503120
Adding box at: x=1  y=1  z=0
Center of solvent box is: -9.432422, -9.239054, 9.503120
Adding box at: x=1  y=1  z=1
Center of solvent box is: -9.432422, -9.239054, -9.503120
  Volume: 49083.880 A^3 
  Total mass 20280.936 amu,  Density 0.686 g/cc
  Added 1094 residues.
> quit
	Quit
log started: Sun Nov  1 20:52:16 2015

Log file: ./leap.log
>> #
>> # ----- leaprc for loading the ff12SB force field
>> # ----- NOTE: this is designed for PDB format 3!
>> #    Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA
>> #
>> #	load atom type hybridizations
>> #
>> addAtomTypes {
>> 	{ "H"   "H" "sp3" }
>> 	{ "HO"  "H" "sp3" }
>> 	{ "HS"  "H" "sp3" }
>> 	{ "H1"  "H" "sp3" }
>> 	{ "H2"  "H" "sp3" }
>> 	{ "H3"  "H" "sp3" }
>> 	{ "H4"  "H" "sp3" }
>> 	{ "H5"  "H" "sp3" }
>> 	{ "HW"  "H" "sp3" }
>> 	{ "HC"  "H" "sp3" }
>> 	{ "HA"  "H" "sp3" }
>> 	{ "HP"  "H" "sp3" }
>> 	{ "HZ"  "H" "sp3" }
>> 	{ "OH"  "O" "sp3" }
>> 	{ "OS"  "O" "sp3" }
>> 	{ "O"   "O" "sp2" }
>> 	{ "O2"  "O" "sp2" }
>> 	{ "OP"  "O" "sp2" }
>> 	{ "OW"  "O" "sp3" }
>> 	{ "CT"  "C" "sp3" }
>> 	{ "CX"  "C" "sp3" }
>> 	{ "C8"  "C" "sp3" }
>> 	{ "2C"  "C" "sp3" }
>> 	{ "3C"  "C" "sp3" }
>> 	{ "CH"  "C" "sp3" }
>> 	{ "CS"  "C" "sp2" }
>> 	{ "C"   "C" "sp2" }
>> 	{ "CO"   "C" "sp2" }
>> 	{ "C*"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CB"  "C" "sp2" }
>> 	{ "CC"  "C" "sp2" }
>> 	{ "CN"  "C" "sp2" }
>> 	{ "CM"  "C" "sp2" }
>> 	{ "CK"  "C" "sp2" }
>> 	{ "CQ"  "C" "sp2" }
>> 	{ "CD"  "C" "sp2" }
>> 	{ "C5"  "C" "sp2" }
>> 	{ "C4"  "C" "sp2" }
>> 	{ "CP"  "C" "sp2" }
>> 	{ "CI"  "C" "sp3" }
>> 	{ "CJ"  "C" "sp2" }
>> 	{ "CW"  "C" "sp2" }
>> 	{ "CV"  "C" "sp2" }
>> 	{ "CR"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CY"  "C" "sp2" }
>> 	{ "C0"  "Ca" "sp3" }
>> 	{ "MG"  "Mg" "sp3" }
>> 	{ "N"   "N" "sp2" }
>> 	{ "NA"  "N" "sp2" }
>> 	{ "N2"  "N" "sp2" }
>> 	{ "N*"  "N" "sp2" }
>> 	{ "NP"  "N" "sp2" }
>> 	{ "NQ"  "N" "sp2" }
>> 	{ "NB"  "N" "sp2" }
>> 	{ "NC"  "N" "sp2" }
>> 	{ "NT"  "N" "sp3" }
>> 	{ "NY"  "N" "sp2" }
>> 	{ "N3"  "N" "sp3" }
>> 	{ "S"   "S" "sp3" }
>> 	{ "SH"  "S" "sp3" }
>> 	{ "P"   "P" "sp3" }
>> 	{ "LP"  ""  "sp3" }
>> 	{ "EP"  ""  "sp3" }
>> 	{ "F"   "F" "sp3" }
>> 	{ "Cl"  "Cl" "sp3" }
>> 	{ "Br"  "Br" "sp3" }
>> 	{ "I"   "I"  "sp3" }
>> 	{ "F-"   "F" "sp3" }
>> 	{ "Cl-"  "Cl" "sp3" }
>> 	{ "Br-"  "Br" "sp3" }
>> 	{ "I-"   "I"  "sp3" }
>> 	{ "Li+"  "Li"  "sp3" }
>> 	{ "Na+"  "Na"  "sp3" }
>> 	{ "K+"  "K"  "sp3" }
>> 	{ "Rb+"  "Rb"  "sp3" }
>> 	{ "Cs+"  "Cs"  "sp3" }
>> 	{ "Mg+"  "Mg"  "sp3" }
>> # glycam
>> 	{ "OG"  "O" "sp3" }
>> 	{ "OL"  "O" "sp3" }
>> 	{ "AC"  "C" "sp3" }
>> 	{ "EC"  "C" "sp3" }
>> }
>> #
>> #	Load the main parameter set.
>> #
>> parm10 = loadamberparams parm10.dat
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
(UNKNOWN ATOM TYPE: Zn)
(UNKNOWN ATOM TYPE: EP)
>> frcmod12SB = loadamberparams frcmod.ff12SB
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff12SB
Reading force field modification type file (frcmod)
Reading title:
ff12SB protein backbone and sidechain parameters
>> #
>> #	Load main chain and terminating amino acid libraries, nucleic acids
>> #
>> loadOff amino12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/amino12.lib
Loading: ALA
Loading: ARG
Loading: ASH
Loading: ASN
Loading: ASP
Loading: CYM
Loading: CYS
Loading: CYX
Loading: GLH
Loading: GLN
Loading: GLU
Loading: GLY
Loading: HID
Loading: HIE
Loading: HIP
Loading: HYP
Loading: ILE
Loading: LEU
Loading: LYN
Loading: LYS
Loading: MET
Loading: PHE
Loading: PRO
Loading: SER
Loading: THR
Loading: TRP
Loading: TYR
Loading: VAL
>> loadOff aminoct12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminoct12.lib
Loading: CALA
Loading: CARG
Loading: CASN
Loading: CASP
Loading: CCYS
Loading: CCYX
Loading: CGLN
Loading: CGLU
Loading: CGLY
Loading: CHID
Loading: CHIE
Loading: CHIP
Loading: CHYP
Loading: CILE
Loading: CLEU
Loading: CLYS
Loading: CMET
Loading: CPHE
Loading: CPRO
Loading: CSER
Loading: CTHR
Loading: CTRP
Loading: CTYR
Loading: CVAL
Loading: NHE
Loading: NME
>> loadOff aminont12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminont12.lib
Loading: ACE
Loading: NALA
Loading: NARG
Loading: NASN
Loading: NASP
Loading: NCYS
Loading: NCYX
Loading: NGLN
Loading: NGLU
Loading: NGLY
Loading: NHID
Loading: NHIE
Loading: NHIP
Loading: NILE
Loading: NLEU
Loading: NLYS
Loading: NMET
Loading: NPHE
Loading: NPRO
Loading: NSER
Loading: NTHR
Loading: NTRP
Loading: NTYR
Loading: NVAL
>> loadOff nucleic12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/nucleic12.lib
Loading: A
Loading: A3
Loading: A5
Loading: AN
Loading: C
Loading: C3
Loading: C5
Loading: CN
Loading: DA
Loading: DA3
Loading: DA5
Loading: DAN
Loading: DC
Loading: DC3
Loading: DC5
Loading: DCN
Loading: DG
Loading: DG3
Loading: DG5
Loading: DGN
Loading: DT
Loading: DT3
Loading: DT5
Loading: DTN
Loading: G
Loading: G3
Loading: G5
Loading: GN
Loading: OHE
Loading: U
Loading: U3
Loading: U5
Loading: UN
>> #
>> #       Load water and ions
>> # 
>> loadOff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
>> loadOff solvents.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: MEOHBOX
Loading: NMABOX
Loading: OPC
Loading: OPCBOX
Loading: PL3
Loading: POL3BOX
Loading: QSPCFWBOX
Loading: SPC
Loading: SPCBOX
Loading: SPCFWBOX
Loading: SPF
Loading: SPG
Loading: T4E
Loading: TIP3PBOX
Loading: TIP3PFBOX
Loading: TIP4PBOX
Loading: TIP4PEWBOX
Loading: TIP5PBOX
Loading: TP3
Loading: TP4
Loading: TP5
Loading: TPF
>> HOH = TP3
>> WAT = TP3
>> 
>> #
>> #	Define the PDB name map for the amino acids and nucleic acids
>> #     (note: no NHYP!  use neutral form for now)
>> #
>> addPdbResMap {
>>   { 0 "HYP" "HYP"  } { 1 "HYP" "CHYP" }
>>   { 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
>>   { 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
>>   { 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
>>   { 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
>>   { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
>>   { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
>>   { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
>>   { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
>>   { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
>>   { 0 "HID" "NHID" } { 1 "HID" "CHID" }
>>   { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
>>   { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
>>   { 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
>>   { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
>>   { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
>>   { 0 "MET" "NMET" } { 1 "MET" "CMET" }
>>   { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
>>   { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
>>   { 0 "SER" "NSER" } { 1 "SER" "CSER" }
>>   { 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
>>   { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
>>   { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
>>   { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
>>   { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
>>   { 0 "G" "G5"  } { 1 "G" "G3"  } 
>>   { 0 "A" "A5"  } { 1 "A" "A3"  } 
>>   { 0 "C" "C5"  } { 1 "C" "C3"  } 
>>   { 0 "U" "U5"  } { 1 "U" "U3"  } 
>>   { 0 "DG" "DG5"  } { 1 "DG" "DG3"  }  
>>   { 0 "DA" "DA5"  } { 1 "DA" "DA3"  }  
>>   { 0 "DC" "DC5"  } { 1 "DC" "DC3"  }  
>>   { 0 "DT" "DT5"  } { 1 "DT" "DT3"  }  
>> #  some old Amber residue names for RNA:
>>   { 0  "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" }
>>   { 0  "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" }
>>   { 0  "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" }
>>   { 0  "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" }
>> #  some really old Amber residue names, assuming DNA:
>>   { 0 "GUA" "DG5"  } { 1 "GUA" "DG3"  } { "GUA" "DG" }
>>   { 0 "ADE" "DA5"  } { 1 "ADE" "DA3"  } { "ADE" "DA" }
>>   { 0 "CYT" "DC5"  } { 1 "CYT" "DC3"  } { "CYT" "DC" }
>>   { 0 "THY" "DT5"  } { 1 "THY" "DT3"  } { "THY" "DT" }
>> #  uncomment out the following if you have this old style RNA files:
>> # { 0 "GUA" "G5"  } { 1 "GUA" "G3"  } { "GUA" "G" }
>> # { 0 "ADE" "A5"  } { 1 "ADE" "A3"  } { "ADE" "A" }
>> # { 0 "CYT" "C5"  } { 1 "CYT" "C3"  } { "CYT" "C" }
>> # { 0 "URA" "R5"  } { 1 "URA" "R3"  } { "URA" "R" }
>> 
>> }
>> 
>> #  try to be good about reading in really old atom names as well:
>> addPdbAtomMap {
>>   { "O5*" "O5'" }
>>   { "C5*" "C5'" }
>>   { "C4*" "C4'" }
>>   { "O4*" "O4'" }
>>   { "C3*" "C3'" }
>>   { "O3*" "O3'" }
>>   { "C2*" "C2'" }
>>   { "O2*" "O2'" }
>>   { "C1*" "C1'" }
>>   { "C5M" "C7"  }
>>   { "H1*" "H1'" }
>>   { "H2*1" "H2'" }
>>   { "H2*2" "H2''" }
>>   { "HO*2" "HO2'" }
>>   { "H2'1" "H2'" }
>>   { "H2'2" "H2''" }
>>   { "H3*" "H3'" }
>>   { "H4*" "H4'" }
>>   { "H5*1" "H5'" }
>>   { "H5*2" "H5''" }
>>   { "H5'1" "H5'" }
>>   { "H5'2" "H5''" }
>>   { "HO'2" "HO2'" }
>>   { "H5T"  "HO5'" }
>>   { "H3T"  "HO3'" }
>>   { "O1'" "O4'" }
>>   { "OA"  "OP1" }
>>   { "OB"  "OP2" }
>>   { "O1P" "OP1" }
>>   { "O2P" "OP2" }
>> }
>> 
>> #
>> # assume that most often proteins use HIE
>> #
>> NHIS = NHIE
>> HIS = HIE
>> CHIS = CHIE
> 
> loadoff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
> loadamberparams frcmod.opc
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.opc
Reading force field modification type file (frcmod)
Reading title:
Parameters for OPC water (JPCL, 2014, 5 (21), pp 3863–3871) 
(UNKNOWN ATOM TYPE: EP)
> loadamberparams frcmod.ionsjc_tip4pew
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip4pew
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP4P/EW water from Joung & Cheatham JPCB (2008)
> 
> m = loadpdb init.pdb
Loading PDB file: ./init.pdb
Enter zPdbReadScan from call depth  0.
Exit  zPdbReadScan from call depth  0.
Matching PDB residue names to LEaP variables.
(Residue 0: A5, Terminal/beginning, was not found in name map.)
(Residue 1: C3, Terminal/last, was not found in name map.)
Joining A5 - C3
  total atoms in file: 63
> 
> 
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.131155 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<H4' 9>
Warning: Close contact of 1.307451 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<C4' 8>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> solvatebox m OPCBOX 10.65 iso
  Solute vdw bounding box:              12.265 11.150 10.292
  Total bounding box for atom centers:  33.565 33.565 33.565
      (box expansion for 'iso' is   9.9%)
  Solvent unit box:                     18.865 18.478 19.006
The number of boxes:  x= 2  y= 2  z= 2
Adding box at: x=0  y=0  z=0
Center of solvent box is: 9.432422, 9.239054, 9.503120
Adding box at: x=0  y=0  z=1
Center of solvent box is: 9.432422, 9.239054, -9.503120
Adding box at: x=0  y=1  z=0
Center of solvent box is: 9.432422, -9.239054, 9.503120
Adding box at: x=0  y=1  z=1
Center of solvent box is: 9.432422, -9.239054, -9.503120
Adding box at: x=1  y=0  z=0
Center of solvent box is: -9.432422, 9.239054, 9.503120
Adding box at: x=1  y=0  z=1
Center of solvent box is: -9.432422, 9.239054, -9.503120
Adding box at: x=1  y=1  z=0
Center of solvent box is: -9.432422, -9.239054, 9.503120
Adding box at: x=1  y=1  z=1
Center of solvent box is: -9.432422, -9.239054, -9.503120
  Volume: 48540.290 A^3 
  Total mass 19992.680 amu,  Density 0.684 g/cc
  Added 1078 residues.
> quit
	Quit
log started: Sun Nov  1 20:52:16 2015

Log file: ./leap.log
>> #
>> # ----- leaprc for loading the ff12SB force field
>> # ----- NOTE: this is designed for PDB format 3!
>> #    Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA
>> #
>> #	load atom type hybridizations
>> #
>> addAtomTypes {
>> 	{ "H"   "H" "sp3" }
>> 	{ "HO"  "H" "sp3" }
>> 	{ "HS"  "H" "sp3" }
>> 	{ "H1"  "H" "sp3" }
>> 	{ "H2"  "H" "sp3" }
>> 	{ "H3"  "H" "sp3" }
>> 	{ "H4"  "H" "sp3" }
>> 	{ "H5"  "H" "sp3" }
>> 	{ "HW"  "H" "sp3" }
>> 	{ "HC"  "H" "sp3" }
>> 	{ "HA"  "H" "sp3" }
>> 	{ "HP"  "H" "sp3" }
>> 	{ "HZ"  "H" "sp3" }
>> 	{ "OH"  "O" "sp3" }
>> 	{ "OS"  "O" "sp3" }
>> 	{ "O"   "O" "sp2" }
>> 	{ "O2"  "O" "sp2" }
>> 	{ "OP"  "O" "sp2" }
>> 	{ "OW"  "O" "sp3" }
>> 	{ "CT"  "C" "sp3" }
>> 	{ "CX"  "C" "sp3" }
>> 	{ "C8"  "C" "sp3" }
>> 	{ "2C"  "C" "sp3" }
>> 	{ "3C"  "C" "sp3" }
>> 	{ "CH"  "C" "sp3" }
>> 	{ "CS"  "C" "sp2" }
>> 	{ "C"   "C" "sp2" }
>> 	{ "CO"   "C" "sp2" }
>> 	{ "C*"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CB"  "C" "sp2" }
>> 	{ "CC"  "C" "sp2" }
>> 	{ "CN"  "C" "sp2" }
>> 	{ "CM"  "C" "sp2" }
>> 	{ "CK"  "C" "sp2" }
>> 	{ "CQ"  "C" "sp2" }
>> 	{ "CD"  "C" "sp2" }
>> 	{ "C5"  "C" "sp2" }
>> 	{ "C4"  "C" "sp2" }
>> 	{ "CP"  "C" "sp2" }
>> 	{ "CI"  "C" "sp3" }
>> 	{ "CJ"  "C" "sp2" }
>> 	{ "CW"  "C" "sp2" }
>> 	{ "CV"  "C" "sp2" }
>> 	{ "CR"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CY"  "C" "sp2" }
>> 	{ "C0"  "Ca" "sp3" }
>> 	{ "MG"  "Mg" "sp3" }
>> 	{ "N"   "N" "sp2" }
>> 	{ "NA"  "N" "sp2" }
>> 	{ "N2"  "N" "sp2" }
>> 	{ "N*"  "N" "sp2" }
>> 	{ "NP"  "N" "sp2" }
>> 	{ "NQ"  "N" "sp2" }
>> 	{ "NB"  "N" "sp2" }
>> 	{ "NC"  "N" "sp2" }
>> 	{ "NT"  "N" "sp3" }
>> 	{ "NY"  "N" "sp2" }
>> 	{ "N3"  "N" "sp3" }
>> 	{ "S"   "S" "sp3" }
>> 	{ "SH"  "S" "sp3" }
>> 	{ "P"   "P" "sp3" }
>> 	{ "LP"  ""  "sp3" }
>> 	{ "EP"  ""  "sp3" }
>> 	{ "F"   "F" "sp3" }
>> 	{ "Cl"  "Cl" "sp3" }
>> 	{ "Br"  "Br" "sp3" }
>> 	{ "I"   "I"  "sp3" }
>> 	{ "F-"   "F" "sp3" }
>> 	{ "Cl-"  "Cl" "sp3" }
>> 	{ "Br-"  "Br" "sp3" }
>> 	{ "I-"   "I"  "sp3" }
>> 	{ "Li+"  "Li"  "sp3" }
>> 	{ "Na+"  "Na"  "sp3" }
>> 	{ "K+"  "K"  "sp3" }
>> 	{ "Rb+"  "Rb"  "sp3" }
>> 	{ "Cs+"  "Cs"  "sp3" }
>> 	{ "Mg+"  "Mg"  "sp3" }
>> # glycam
>> 	{ "OG"  "O" "sp3" }
>> 	{ "OL"  "O" "sp3" }
>> 	{ "AC"  "C" "sp3" }
>> 	{ "EC"  "C" "sp3" }
>> }
>> #
>> #	Load the main parameter set.
>> #
>> parm10 = loadamberparams parm10.dat
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
(UNKNOWN ATOM TYPE: Zn)
(UNKNOWN ATOM TYPE: EP)
>> frcmod12SB = loadamberparams frcmod.ff12SB
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff12SB
Reading force field modification type file (frcmod)
Reading title:
ff12SB protein backbone and sidechain parameters
>> #
>> #	Load main chain and terminating amino acid libraries, nucleic acids
>> #
>> loadOff amino12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/amino12.lib
Loading: ALA
Loading: ARG
Loading: ASH
Loading: ASN
Loading: ASP
Loading: CYM
Loading: CYS
Loading: CYX
Loading: GLH
Loading: GLN
Loading: GLU
Loading: GLY
Loading: HID
Loading: HIE
Loading: HIP
Loading: HYP
Loading: ILE
Loading: LEU
Loading: LYN
Loading: LYS
Loading: MET
Loading: PHE
Loading: PRO
Loading: SER
Loading: THR
Loading: TRP
Loading: TYR
Loading: VAL
>> loadOff aminoct12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminoct12.lib
Loading: CALA
Loading: CARG
Loading: CASN
Loading: CASP
Loading: CCYS
Loading: CCYX
Loading: CGLN
Loading: CGLU
Loading: CGLY
Loading: CHID
Loading: CHIE
Loading: CHIP
Loading: CHYP
Loading: CILE
Loading: CLEU
Loading: CLYS
Loading: CMET
Loading: CPHE
Loading: CPRO
Loading: CSER
Loading: CTHR
Loading: CTRP
Loading: CTYR
Loading: CVAL
Loading: NHE
Loading: NME
>> loadOff aminont12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminont12.lib
Loading: ACE
Loading: NALA
Loading: NARG
Loading: NASN
Loading: NASP
Loading: NCYS
Loading: NCYX
Loading: NGLN
Loading: NGLU
Loading: NGLY
Loading: NHID
Loading: NHIE
Loading: NHIP
Loading: NILE
Loading: NLEU
Loading: NLYS
Loading: NMET
Loading: NPHE
Loading: NPRO
Loading: NSER
Loading: NTHR
Loading: NTRP
Loading: NTYR
Loading: NVAL
>> loadOff nucleic12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/nucleic12.lib
Loading: A
Loading: A3
Loading: A5
Loading: AN
Loading: C
Loading: C3
Loading: C5
Loading: CN
Loading: DA
Loading: DA3
Loading: DA5
Loading: DAN
Loading: DC
Loading: DC3
Loading: DC5
Loading: DCN
Loading: DG
Loading: DG3
Loading: DG5
Loading: DGN
Loading: DT
Loading: DT3
Loading: DT5
Loading: DTN
Loading: G
Loading: G3
Loading: G5
Loading: GN
Loading: OHE
Loading: U
Loading: U3
Loading: U5
Loading: UN
>> #
>> #       Load water and ions
>> # 
>> loadOff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
>> loadOff solvents.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: MEOHBOX
Loading: NMABOX
Loading: OPC
Loading: OPCBOX
Loading: PL3
Loading: POL3BOX
Loading: QSPCFWBOX
Loading: SPC
Loading: SPCBOX
Loading: SPCFWBOX
Loading: SPF
Loading: SPG
Loading: T4E
Loading: TIP3PBOX
Loading: TIP3PFBOX
Loading: TIP4PBOX
Loading: TIP4PEWBOX
Loading: TIP5PBOX
Loading: TP3
Loading: TP4
Loading: TP5
Loading: TPF
>> HOH = TP3
>> WAT = TP3
>> 
>> #
>> #	Define the PDB name map for the amino acids and nucleic acids
>> #     (note: no NHYP!  use neutral form for now)
>> #
>> addPdbResMap {
>>   { 0 "HYP" "HYP"  } { 1 "HYP" "CHYP" }
>>   { 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
>>   { 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
>>   { 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
>>   { 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
>>   { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
>>   { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
>>   { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
>>   { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
>>   { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
>>   { 0 "HID" "NHID" } { 1 "HID" "CHID" }
>>   { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
>>   { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
>>   { 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
>>   { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
>>   { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
>>   { 0 "MET" "NMET" } { 1 "MET" "CMET" }
>>   { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
>>   { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
>>   { 0 "SER" "NSER" } { 1 "SER" "CSER" }
>>   { 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
>>   { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
>>   { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
>>   { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
>>   { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
>>   { 0 "G" "G5"  } { 1 "G" "G3"  } 
>>   { 0 "A" "A5"  } { 1 "A" "A3"  } 
>>   { 0 "C" "C5"  } { 1 "C" "C3"  } 
>>   { 0 "U" "U5"  } { 1 "U" "U3"  } 
>>   { 0 "DG" "DG5"  } { 1 "DG" "DG3"  }  
>>   { 0 "DA" "DA5"  } { 1 "DA" "DA3"  }  
>>   { 0 "DC" "DC5"  } { 1 "DC" "DC3"  }  
>>   { 0 "DT" "DT5"  } { 1 "DT" "DT3"  }  
>> #  some old Amber residue names for RNA:
>>   { 0  "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" }
>>   { 0  "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" }
>>   { 0  "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" }
>>   { 0  "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" }
>> #  some really old Amber residue names, assuming DNA:
>>   { 0 "GUA" "DG5"  } { 1 "GUA" "DG3"  } { "GUA" "DG" }
>>   { 0 "ADE" "DA5"  } { 1 "ADE" "DA3"  } { "ADE" "DA" }
>>   { 0 "CYT" "DC5"  } { 1 "CYT" "DC3"  } { "CYT" "DC" }
>>   { 0 "THY" "DT5"  } { 1 "THY" "DT3"  } { "THY" "DT" }
>> #  uncomment out the following if you have this old style RNA files:
>> # { 0 "GUA" "G5"  } { 1 "GUA" "G3"  } { "GUA" "G" }
>> # { 0 "ADE" "A5"  } { 1 "ADE" "A3"  } { "ADE" "A" }
>> # { 0 "CYT" "C5"  } { 1 "CYT" "C3"  } { "CYT" "C" }
>> # { 0 "URA" "R5"  } { 1 "URA" "R3"  } { "URA" "R" }
>> 
>> }
>> 
>> #  try to be good about reading in really old atom names as well:
>> addPdbAtomMap {
>>   { "O5*" "O5'" }
>>   { "C5*" "C5'" }
>>   { "C4*" "C4'" }
>>   { "O4*" "O4'" }
>>   { "C3*" "C3'" }
>>   { "O3*" "O3'" }
>>   { "C2*" "C2'" }
>>   { "O2*" "O2'" }
>>   { "C1*" "C1'" }
>>   { "C5M" "C7"  }
>>   { "H1*" "H1'" }
>>   { "H2*1" "H2'" }
>>   { "H2*2" "H2''" }
>>   { "HO*2" "HO2'" }
>>   { "H2'1" "H2'" }
>>   { "H2'2" "H2''" }
>>   { "H3*" "H3'" }
>>   { "H4*" "H4'" }
>>   { "H5*1" "H5'" }
>>   { "H5*2" "H5''" }
>>   { "H5'1" "H5'" }
>>   { "H5'2" "H5''" }
>>   { "HO'2" "HO2'" }
>>   { "H5T"  "HO5'" }
>>   { "H3T"  "HO3'" }
>>   { "O1'" "O4'" }
>>   { "OA"  "OP1" }
>>   { "OB"  "OP2" }
>>   { "O1P" "OP1" }
>>   { "O2P" "OP2" }
>> }
>> 
>> #
>> # assume that most often proteins use HIE
>> #
>> NHIS = NHIE
>> HIS = HIE
>> CHIS = CHIE
> 
> loadoff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
> loadamberparams frcmod.opc
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.opc
Reading force field modification type file (frcmod)
Reading title:
Parameters for OPC water (JPCL, 2014, 5 (21), pp 3863–3871) 
(UNKNOWN ATOM TYPE: EP)
> loadamberparams frcmod.ionsjc_tip4pew
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip4pew
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP4P/EW water from Joung & Cheatham JPCB (2008)
> 
> m = loadpdb init.pdb
Loading PDB file: ./init.pdb
Enter zPdbReadScan from call depth  0.
Exit  zPdbReadScan from call depth  0.
Matching PDB residue names to LEaP variables.
(Residue 0: A5, Terminal/beginning, was not found in name map.)
(Residue 1: C3, Terminal/last, was not found in name map.)
Joining A5 - C3
  total atoms in file: 63
> 
> 
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.131155 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<H4' 9>
Warning: Close contact of 1.307451 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<C4' 8>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> solvatebox m OPCBOX 10.66 iso
  Solute vdw bounding box:              12.265 11.150 10.292
  Total bounding box for atom centers:  33.585 33.585 33.585
      (box expansion for 'iso' is   9.9%)
  Solvent unit box:                     18.865 18.478 19.006
The number of boxes:  x= 2  y= 2  z= 2
Adding box at: x=0  y=0  z=0
Center of solvent box is: 9.432422, 9.239054, 9.503120
Adding box at: x=0  y=0  z=1
Center of solvent box is: 9.432422, 9.239054, -9.503120
Adding box at: x=0  y=1  z=0
Center of solvent box is: 9.432422, -9.239054, 9.503120
Adding box at: x=0  y=1  z=1
Center of solvent box is: 9.432422, -9.239054, -9.503120
Adding box at: x=1  y=0  z=0
Center of solvent box is: -9.432422, 9.239054, 9.503120
Adding box at: x=1  y=0  z=1
Center of solvent box is: -9.432422, 9.239054, -9.503120
Adding box at: x=1  y=1  z=0
Center of solvent box is: -9.432422, -9.239054, 9.503120
Adding box at: x=1  y=1  z=1
Center of solvent box is: -9.432422, -9.239054, -9.503120
  Volume: 48622.506 A^3 
  Total mass 20100.776 amu,  Density 0.686 g/cc
  Added 1084 residues.
> quit
	Quit
log started: Sun Nov  1 20:52:17 2015

Log file: ./leap.log
>> #
>> # ----- leaprc for loading the ff12SB force field
>> # ----- NOTE: this is designed for PDB format 3!
>> #    Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA
>> #
>> #	load atom type hybridizations
>> #
>> addAtomTypes {
>> 	{ "H"   "H" "sp3" }
>> 	{ "HO"  "H" "sp3" }
>> 	{ "HS"  "H" "sp3" }
>> 	{ "H1"  "H" "sp3" }
>> 	{ "H2"  "H" "sp3" }
>> 	{ "H3"  "H" "sp3" }
>> 	{ "H4"  "H" "sp3" }
>> 	{ "H5"  "H" "sp3" }
>> 	{ "HW"  "H" "sp3" }
>> 	{ "HC"  "H" "sp3" }
>> 	{ "HA"  "H" "sp3" }
>> 	{ "HP"  "H" "sp3" }
>> 	{ "HZ"  "H" "sp3" }
>> 	{ "OH"  "O" "sp3" }
>> 	{ "OS"  "O" "sp3" }
>> 	{ "O"   "O" "sp2" }
>> 	{ "O2"  "O" "sp2" }
>> 	{ "OP"  "O" "sp2" }
>> 	{ "OW"  "O" "sp3" }
>> 	{ "CT"  "C" "sp3" }
>> 	{ "CX"  "C" "sp3" }
>> 	{ "C8"  "C" "sp3" }
>> 	{ "2C"  "C" "sp3" }
>> 	{ "3C"  "C" "sp3" }
>> 	{ "CH"  "C" "sp3" }
>> 	{ "CS"  "C" "sp2" }
>> 	{ "C"   "C" "sp2" }
>> 	{ "CO"   "C" "sp2" }
>> 	{ "C*"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CB"  "C" "sp2" }
>> 	{ "CC"  "C" "sp2" }
>> 	{ "CN"  "C" "sp2" }
>> 	{ "CM"  "C" "sp2" }
>> 	{ "CK"  "C" "sp2" }
>> 	{ "CQ"  "C" "sp2" }
>> 	{ "CD"  "C" "sp2" }
>> 	{ "C5"  "C" "sp2" }
>> 	{ "C4"  "C" "sp2" }
>> 	{ "CP"  "C" "sp2" }
>> 	{ "CI"  "C" "sp3" }
>> 	{ "CJ"  "C" "sp2" }
>> 	{ "CW"  "C" "sp2" }
>> 	{ "CV"  "C" "sp2" }
>> 	{ "CR"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CY"  "C" "sp2" }
>> 	{ "C0"  "Ca" "sp3" }
>> 	{ "MG"  "Mg" "sp3" }
>> 	{ "N"   "N" "sp2" }
>> 	{ "NA"  "N" "sp2" }
>> 	{ "N2"  "N" "sp2" }
>> 	{ "N*"  "N" "sp2" }
>> 	{ "NP"  "N" "sp2" }
>> 	{ "NQ"  "N" "sp2" }
>> 	{ "NB"  "N" "sp2" }
>> 	{ "NC"  "N" "sp2" }
>> 	{ "NT"  "N" "sp3" }
>> 	{ "NY"  "N" "sp2" }
>> 	{ "N3"  "N" "sp3" }
>> 	{ "S"   "S" "sp3" }
>> 	{ "SH"  "S" "sp3" }
>> 	{ "P"   "P" "sp3" }
>> 	{ "LP"  ""  "sp3" }
>> 	{ "EP"  ""  "sp3" }
>> 	{ "F"   "F" "sp3" }
>> 	{ "Cl"  "Cl" "sp3" }
>> 	{ "Br"  "Br" "sp3" }
>> 	{ "I"   "I"  "sp3" }
>> 	{ "F-"   "F" "sp3" }
>> 	{ "Cl-"  "Cl" "sp3" }
>> 	{ "Br-"  "Br" "sp3" }
>> 	{ "I-"   "I"  "sp3" }
>> 	{ "Li+"  "Li"  "sp3" }
>> 	{ "Na+"  "Na"  "sp3" }
>> 	{ "K+"  "K"  "sp3" }
>> 	{ "Rb+"  "Rb"  "sp3" }
>> 	{ "Cs+"  "Cs"  "sp3" }
>> 	{ "Mg+"  "Mg"  "sp3" }
>> # glycam
>> 	{ "OG"  "O" "sp3" }
>> 	{ "OL"  "O" "sp3" }
>> 	{ "AC"  "C" "sp3" }
>> 	{ "EC"  "C" "sp3" }
>> }
>> #
>> #	Load the main parameter set.
>> #
>> parm10 = loadamberparams parm10.dat
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
(UNKNOWN ATOM TYPE: Zn)
(UNKNOWN ATOM TYPE: EP)
>> frcmod12SB = loadamberparams frcmod.ff12SB
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff12SB
Reading force field modification type file (frcmod)
Reading title:
ff12SB protein backbone and sidechain parameters
>> #
>> #	Load main chain and terminating amino acid libraries, nucleic acids
>> #
>> loadOff amino12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/amino12.lib
Loading: ALA
Loading: ARG
Loading: ASH
Loading: ASN
Loading: ASP
Loading: CYM
Loading: CYS
Loading: CYX
Loading: GLH
Loading: GLN
Loading: GLU
Loading: GLY
Loading: HID
Loading: HIE
Loading: HIP
Loading: HYP
Loading: ILE
Loading: LEU
Loading: LYN
Loading: LYS
Loading: MET
Loading: PHE
Loading: PRO
Loading: SER
Loading: THR
Loading: TRP
Loading: TYR
Loading: VAL
>> loadOff aminoct12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminoct12.lib
Loading: CALA
Loading: CARG
Loading: CASN
Loading: CASP
Loading: CCYS
Loading: CCYX
Loading: CGLN
Loading: CGLU
Loading: CGLY
Loading: CHID
Loading: CHIE
Loading: CHIP
Loading: CHYP
Loading: CILE
Loading: CLEU
Loading: CLYS
Loading: CMET
Loading: CPHE
Loading: CPRO
Loading: CSER
Loading: CTHR
Loading: CTRP
Loading: CTYR
Loading: CVAL
Loading: NHE
Loading: NME
>> loadOff aminont12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminont12.lib
Loading: ACE
Loading: NALA
Loading: NARG
Loading: NASN
Loading: NASP
Loading: NCYS
Loading: NCYX
Loading: NGLN
Loading: NGLU
Loading: NGLY
Loading: NHID
Loading: NHIE
Loading: NHIP
Loading: NILE
Loading: NLEU
Loading: NLYS
Loading: NMET
Loading: NPHE
Loading: NPRO
Loading: NSER
Loading: NTHR
Loading: NTRP
Loading: NTYR
Loading: NVAL
>> loadOff nucleic12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/nucleic12.lib
Loading: A
Loading: A3
Loading: A5
Loading: AN
Loading: C
Loading: C3
Loading: C5
Loading: CN
Loading: DA
Loading: DA3
Loading: DA5
Loading: DAN
Loading: DC
Loading: DC3
Loading: DC5
Loading: DCN
Loading: DG
Loading: DG3
Loading: DG5
Loading: DGN
Loading: DT
Loading: DT3
Loading: DT5
Loading: DTN
Loading: G
Loading: G3
Loading: G5
Loading: GN
Loading: OHE
Loading: U
Loading: U3
Loading: U5
Loading: UN
>> #
>> #       Load water and ions
>> # 
>> loadOff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
>> loadOff solvents.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: MEOHBOX
Loading: NMABOX
Loading: OPC
Loading: OPCBOX
Loading: PL3
Loading: POL3BOX
Loading: QSPCFWBOX
Loading: SPC
Loading: SPCBOX
Loading: SPCFWBOX
Loading: SPF
Loading: SPG
Loading: T4E
Loading: TIP3PBOX
Loading: TIP3PFBOX
Loading: TIP4PBOX
Loading: TIP4PEWBOX
Loading: TIP5PBOX
Loading: TP3
Loading: TP4
Loading: TP5
Loading: TPF
>> HOH = TP3
>> WAT = TP3
>> 
>> #
>> #	Define the PDB name map for the amino acids and nucleic acids
>> #     (note: no NHYP!  use neutral form for now)
>> #
>> addPdbResMap {
>>   { 0 "HYP" "HYP"  } { 1 "HYP" "CHYP" }
>>   { 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
>>   { 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
>>   { 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
>>   { 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
>>   { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
>>   { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
>>   { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
>>   { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
>>   { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
>>   { 0 "HID" "NHID" } { 1 "HID" "CHID" }
>>   { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
>>   { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
>>   { 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
>>   { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
>>   { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
>>   { 0 "MET" "NMET" } { 1 "MET" "CMET" }
>>   { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
>>   { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
>>   { 0 "SER" "NSER" } { 1 "SER" "CSER" }
>>   { 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
>>   { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
>>   { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
>>   { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
>>   { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
>>   { 0 "G" "G5"  } { 1 "G" "G3"  } 
>>   { 0 "A" "A5"  } { 1 "A" "A3"  } 
>>   { 0 "C" "C5"  } { 1 "C" "C3"  } 
>>   { 0 "U" "U5"  } { 1 "U" "U3"  } 
>>   { 0 "DG" "DG5"  } { 1 "DG" "DG3"  }  
>>   { 0 "DA" "DA5"  } { 1 "DA" "DA3"  }  
>>   { 0 "DC" "DC5"  } { 1 "DC" "DC3"  }  
>>   { 0 "DT" "DT5"  } { 1 "DT" "DT3"  }  
>> #  some old Amber residue names for RNA:
>>   { 0  "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" }
>>   { 0  "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" }
>>   { 0  "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" }
>>   { 0  "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" }
>> #  some really old Amber residue names, assuming DNA:
>>   { 0 "GUA" "DG5"  } { 1 "GUA" "DG3"  } { "GUA" "DG" }
>>   { 0 "ADE" "DA5"  } { 1 "ADE" "DA3"  } { "ADE" "DA" }
>>   { 0 "CYT" "DC5"  } { 1 "CYT" "DC3"  } { "CYT" "DC" }
>>   { 0 "THY" "DT5"  } { 1 "THY" "DT3"  } { "THY" "DT" }
>> #  uncomment out the following if you have this old style RNA files:
>> # { 0 "GUA" "G5"  } { 1 "GUA" "G3"  } { "GUA" "G" }
>> # { 0 "ADE" "A5"  } { 1 "ADE" "A3"  } { "ADE" "A" }
>> # { 0 "CYT" "C5"  } { 1 "CYT" "C3"  } { "CYT" "C" }
>> # { 0 "URA" "R5"  } { 1 "URA" "R3"  } { "URA" "R" }
>> 
>> }
>> 
>> #  try to be good about reading in really old atom names as well:
>> addPdbAtomMap {
>>   { "O5*" "O5'" }
>>   { "C5*" "C5'" }
>>   { "C4*" "C4'" }
>>   { "O4*" "O4'" }
>>   { "C3*" "C3'" }
>>   { "O3*" "O3'" }
>>   { "C2*" "C2'" }
>>   { "O2*" "O2'" }
>>   { "C1*" "C1'" }
>>   { "C5M" "C7"  }
>>   { "H1*" "H1'" }
>>   { "H2*1" "H2'" }
>>   { "H2*2" "H2''" }
>>   { "HO*2" "HO2'" }
>>   { "H2'1" "H2'" }
>>   { "H2'2" "H2''" }
>>   { "H3*" "H3'" }
>>   { "H4*" "H4'" }
>>   { "H5*1" "H5'" }
>>   { "H5*2" "H5''" }
>>   { "H5'1" "H5'" }
>>   { "H5'2" "H5''" }
>>   { "HO'2" "HO2'" }
>>   { "H5T"  "HO5'" }
>>   { "H3T"  "HO3'" }
>>   { "O1'" "O4'" }
>>   { "OA"  "OP1" }
>>   { "OB"  "OP2" }
>>   { "O1P" "OP1" }
>>   { "O2P" "OP2" }
>> }
>> 
>> #
>> # assume that most often proteins use HIE
>> #
>> NHIS = NHIE
>> HIS = HIE
>> CHIS = CHIE
> 
> loadoff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
> loadamberparams frcmod.opc
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.opc
Reading force field modification type file (frcmod)
Reading title:
Parameters for OPC water (JPCL, 2014, 5 (21), pp 3863–3871) 
(UNKNOWN ATOM TYPE: EP)
> loadamberparams frcmod.ionsjc_tip4pew
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip4pew
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP4P/EW water from Joung & Cheatham JPCB (2008)
> 
> m = loadpdb init.pdb
Loading PDB file: ./init.pdb
Enter zPdbReadScan from call depth  0.
Exit  zPdbReadScan from call depth  0.
Matching PDB residue names to LEaP variables.
(Residue 0: A5, Terminal/beginning, was not found in name map.)
(Residue 1: C3, Terminal/last, was not found in name map.)
Joining A5 - C3
  total atoms in file: 63
> 
> 
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.131155 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<H4' 9>
Warning: Close contact of 1.307451 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<C4' 8>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> solvateoct m OPCBOX 10.66 iso
Scaling up box by a factor of 1.255501 to meet diagonal cut criterion
  Solute vdw bounding box:              12.265 11.150 10.292
  Total bounding box for atom centers:  39.032 39.032 39.032
      (box expansion for 'iso' is   8.4%)
  Solvent unit box:                     18.865 18.478 19.006
The number of boxes:  x= 3  y= 3  z= 3
Adding box at: x=0  y=0  z=0
Center of solvent box is: 18.864844, 18.478108, 19.006241
Adding box at: x=0  y=0  z=1
Center of solvent box is: 18.864844, 18.478108, 0.000000
Adding box at: x=0  y=0  z=2
Center of solvent box is: 18.864844, 18.478108, -19.006241
Adding box at: x=0  y=1  z=0
Center of solvent box is: 18.864844, 0.000000, 19.006241
Adding box at: x=0  y=1  z=1
Center of solvent box is: 18.864844, 0.000000, 0.000000
Adding box at: x=0  y=1  z=2
Center of solvent box is: 18.864844, 0.000000, -19.006241
Adding box at: x=0  y=2  z=0
Center of solvent box is: 18.864844, -18.478108, 19.006241
Adding box at: x=0  y=2  z=1
Center of solvent box is: 18.864844, -18.478108, 0.000000
Adding box at: x=0  y=2  z=2
Center of solvent box is: 18.864844, -18.478108, -19.006241
Adding box at: x=1  y=0  z=0
Center of solvent box is: 0.000000, 18.478108, 19.006241
Adding box at: x=1  y=0  z=1
Center of solvent box is: 0.000000, 18.478108, 0.000000
Adding box at: x=1  y=0  z=2
Center of solvent box is: 0.000000, 18.478108, -19.006241
Adding box at: x=1  y=1  z=0
Center of solvent box is: 0.000000, 0.000000, 19.006241
Adding box at: x=1  y=1  z=1
Center of solvent box is: 0.000000, 0.000000, 0.000000
Adding box at: x=1  y=1  z=2
Center of solvent box is: 0.000000, 0.000000, -19.006241
Adding box at: x=1  y=2  z=0
Center of solvent box is: 0.000000, -18.478108, 19.006241
Adding box at: x=1  y=2  z=1
Center of solvent box is: 0.000000, -18.478108, 0.000000
Adding box at: x=1  y=2  z=2
Center of solvent box is: 0.000000, -18.478108, -19.006241
Adding box at: x=2  y=0  z=0
Center of solvent box is: -18.864844, 18.478108, 19.006241
Adding box at: x=2  y=0  z=1
Center of solvent box is: -18.864844, 18.478108, 0.000000
Adding box at: x=2  y=0  z=2
Center of solvent box is: -18.864844, 18.478108, -19.006241
Adding box at: x=2  y=1  z=0
Center of solvent box is: -18.864844, 0.000000, 19.006241
Adding box at: x=2  y=1  z=1
Center of solvent box is: -18.864844, 0.000000, 0.000000
Adding box at: x=2  y=1  z=2
Center of solvent box is: -18.864844, 0.000000, -19.006241
Adding box at: x=2  y=2  z=0
Center of solvent box is: -18.864844, -18.478108, 19.006241
Adding box at: x=2  y=2  z=1
Center of solvent box is: -18.864844, -18.478108, 0.000000
Adding box at: x=2  y=2  z=2
Center of solvent box is: -18.864844, -18.478108, -19.006241
  Volume: 32076.638 A^3 (oct)
  Total mass 15975.112 amu,  Density 0.827 g/cc
  Added 855 residues.
> 
> addions m Na+ 0
1 Na+ ion required to neutralize.
Adding 1 counter ions to "m" using 1A grid
Total solute charge:  -1.00  Max atom radius:   2.10
Grid extends from solute vdw + 1.23  to  7.33
Box:
   enclosing:  -12.17 -12.51 -11.93   11.12 10.79 11.67
   sized:			      19.83 19.49 20.07
   edge:        32.00
Resolution:      1.00 Angstrom.
Tree depth: 5
grid build: 0 sec
Volume = 15.67% of box, grid points 5136
Solvent present: replacing closest with ion
	 when steric overlaps occur
Calculating grid charges
charges: 0 sec
(Replacing solvent molecule)
Placed Na+ in m at (-4.35, 7.22, -4.33).

Done adding ions.
> addions m Na+ 5 Cl- 5
Na+ has a charge of 0.
Adding the ions anyway.
Adding 10 counter ions to "m" using 1A grid
Total solute charge:   0.00  Max atom radius:   2.10
Grid extends from solute vdw + 6.14  to  12.24
Box:
   enclosing:  -17.08 -17.42 -16.84   16.03 19.46 16.58
   sized:			      46.92 46.58 47.16
   edge:        64.00
Resolution:      1.00 Angstrom.
Tree depth: 6
grid build: 0 sec
Volume =  5.01% of box, grid points 13140
Solvent present: replacing closest with ion
	 when steric overlaps occur
Calculating grid charges
charges: 0 sec
(Replacing solvent molecule)
Placed Na+ in m at (-4.69, -8.58, -3.07).
(Replacing solvent molecule)
Placed Cl- in m at (-2.47, -14.18, -4.79).
(Replacing solvent molecule)
Placed Na+ in m at (-0.97, -11.42, -1.40).
(Replacing solvent molecule)
Placed Cl- in m at (-5.30, -11.19, 0.90).
(Replacing solvent molecule)
Placed Na+ in m at (-1.42, -11.98, -6.95).
(Replacing solvent molecule)
Placed Cl- in m at (3.06, -11.72, -4.85).
(Replacing solvent molecule)
Placed Na+ in m at (7.33, -13.47, -5.37).
(Replacing solvent molecule)
Placed Cl- in m at (2.47, -10.50, -7.56).
(Replacing solvent molecule)
Placed Na+ in m at (4.34, -8.56, -6.33).
(Replacing solvent molecule)
Placed Cl- in m at (11.21, -9.63, -6.55).

Done adding ions.
> 
> saveamberparm m full.topo non-randomized.crds
Checking Unit.

 -- ignoring the warnings.

Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 ** Warning: No sp2 improper torsion term for  N*-CB-CB-NC
        atoms are: N9 C5 C4 N3
 ** Warning: No sp2 improper torsion term for  NB-CA-CB-CB
        atoms are: N7 C6 C5 C4
 total 11 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
 (no restraints)
> quit
	Quit
log started: Sun Nov  1 20:52:17 2015

Log file: ./leap.log
>> #
>> # ----- leaprc for loading the ff12SB force field
>> # ----- NOTE: this is designed for PDB format 3!
>> #    Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA
>> #
>> #	load atom type hybridizations
>> #
>> addAtomTypes {
>> 	{ "H"   "H" "sp3" }
>> 	{ "HO"  "H" "sp3" }
>> 	{ "HS"  "H" "sp3" }
>> 	{ "H1"  "H" "sp3" }
>> 	{ "H2"  "H" "sp3" }
>> 	{ "H3"  "H" "sp3" }
>> 	{ "H4"  "H" "sp3" }
>> 	{ "H5"  "H" "sp3" }
>> 	{ "HW"  "H" "sp3" }
>> 	{ "HC"  "H" "sp3" }
>> 	{ "HA"  "H" "sp3" }
>> 	{ "HP"  "H" "sp3" }
>> 	{ "HZ"  "H" "sp3" }
>> 	{ "OH"  "O" "sp3" }
>> 	{ "OS"  "O" "sp3" }
>> 	{ "O"   "O" "sp2" }
>> 	{ "O2"  "O" "sp2" }
>> 	{ "OP"  "O" "sp2" }
>> 	{ "OW"  "O" "sp3" }
>> 	{ "CT"  "C" "sp3" }
>> 	{ "CX"  "C" "sp3" }
>> 	{ "C8"  "C" "sp3" }
>> 	{ "2C"  "C" "sp3" }
>> 	{ "3C"  "C" "sp3" }
>> 	{ "CH"  "C" "sp3" }
>> 	{ "CS"  "C" "sp2" }
>> 	{ "C"   "C" "sp2" }
>> 	{ "CO"   "C" "sp2" }
>> 	{ "C*"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CB"  "C" "sp2" }
>> 	{ "CC"  "C" "sp2" }
>> 	{ "CN"  "C" "sp2" }
>> 	{ "CM"  "C" "sp2" }
>> 	{ "CK"  "C" "sp2" }
>> 	{ "CQ"  "C" "sp2" }
>> 	{ "CD"  "C" "sp2" }
>> 	{ "C5"  "C" "sp2" }
>> 	{ "C4"  "C" "sp2" }
>> 	{ "CP"  "C" "sp2" }
>> 	{ "CI"  "C" "sp3" }
>> 	{ "CJ"  "C" "sp2" }
>> 	{ "CW"  "C" "sp2" }
>> 	{ "CV"  "C" "sp2" }
>> 	{ "CR"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CY"  "C" "sp2" }
>> 	{ "C0"  "Ca" "sp3" }
>> 	{ "MG"  "Mg" "sp3" }
>> 	{ "N"   "N" "sp2" }
>> 	{ "NA"  "N" "sp2" }
>> 	{ "N2"  "N" "sp2" }
>> 	{ "N*"  "N" "sp2" }
>> 	{ "NP"  "N" "sp2" }
>> 	{ "NQ"  "N" "sp2" }
>> 	{ "NB"  "N" "sp2" }
>> 	{ "NC"  "N" "sp2" }
>> 	{ "NT"  "N" "sp3" }
>> 	{ "NY"  "N" "sp2" }
>> 	{ "N3"  "N" "sp3" }
>> 	{ "S"   "S" "sp3" }
>> 	{ "SH"  "S" "sp3" }
>> 	{ "P"   "P" "sp3" }
>> 	{ "LP"  ""  "sp3" }
>> 	{ "EP"  ""  "sp3" }
>> 	{ "F"   "F" "sp3" }
>> 	{ "Cl"  "Cl" "sp3" }
>> 	{ "Br"  "Br" "sp3" }
>> 	{ "I"   "I"  "sp3" }
>> 	{ "F-"   "F" "sp3" }
>> 	{ "Cl-"  "Cl" "sp3" }
>> 	{ "Br-"  "Br" "sp3" }
>> 	{ "I-"   "I"  "sp3" }
>> 	{ "Li+"  "Li"  "sp3" }
>> 	{ "Na+"  "Na"  "sp3" }
>> 	{ "K+"  "K"  "sp3" }
>> 	{ "Rb+"  "Rb"  "sp3" }
>> 	{ "Cs+"  "Cs"  "sp3" }
>> 	{ "Mg+"  "Mg"  "sp3" }
>> # glycam
>> 	{ "OG"  "O" "sp3" }
>> 	{ "OL"  "O" "sp3" }
>> 	{ "AC"  "C" "sp3" }
>> 	{ "EC"  "C" "sp3" }
>> }
>> #
>> #	Load the main parameter set.
>> #
>> parm10 = loadamberparams parm10.dat
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
(UNKNOWN ATOM TYPE: Zn)
(UNKNOWN ATOM TYPE: EP)
>> frcmod12SB = loadamberparams frcmod.ff12SB
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff12SB
Reading force field modification type file (frcmod)
Reading title:
ff12SB protein backbone and sidechain parameters
>> #
>> #	Load main chain and terminating amino acid libraries, nucleic acids
>> #
>> loadOff amino12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/amino12.lib
Loading: ALA
Loading: ARG
Loading: ASH
Loading: ASN
Loading: ASP
Loading: CYM
Loading: CYS
Loading: CYX
Loading: GLH
Loading: GLN
Loading: GLU
Loading: GLY
Loading: HID
Loading: HIE
Loading: HIP
Loading: HYP
Loading: ILE
Loading: LEU
Loading: LYN
Loading: LYS
Loading: MET
Loading: PHE
Loading: PRO
Loading: SER
Loading: THR
Loading: TRP
Loading: TYR
Loading: VAL
>> loadOff aminoct12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminoct12.lib
Loading: CALA
Loading: CARG
Loading: CASN
Loading: CASP
Loading: CCYS
Loading: CCYX
Loading: CGLN
Loading: CGLU
Loading: CGLY
Loading: CHID
Loading: CHIE
Loading: CHIP
Loading: CHYP
Loading: CILE
Loading: CLEU
Loading: CLYS
Loading: CMET
Loading: CPHE
Loading: CPRO
Loading: CSER
Loading: CTHR
Loading: CTRP
Loading: CTYR
Loading: CVAL
Loading: NHE
Loading: NME
>> loadOff aminont12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminont12.lib
Loading: ACE
Loading: NALA
Loading: NARG
Loading: NASN
Loading: NASP
Loading: NCYS
Loading: NCYX
Loading: NGLN
Loading: NGLU
Loading: NGLY
Loading: NHID
Loading: NHIE
Loading: NHIP
Loading: NILE
Loading: NLEU
Loading: NLYS
Loading: NMET
Loading: NPHE
Loading: NPRO
Loading: NSER
Loading: NTHR
Loading: NTRP
Loading: NTYR
Loading: NVAL
>> loadOff nucleic12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/nucleic12.lib
Loading: A
Loading: A3
Loading: A5
Loading: AN
Loading: C
Loading: C3
Loading: C5
Loading: CN
Loading: DA
Loading: DA3
Loading: DA5
Loading: DAN
Loading: DC
Loading: DC3
Loading: DC5
Loading: DCN
Loading: DG
Loading: DG3
Loading: DG5
Loading: DGN
Loading: DT
Loading: DT3
Loading: DT5
Loading: DTN
Loading: G
Loading: G3
Loading: G5
Loading: GN
Loading: OHE
Loading: U
Loading: U3
Loading: U5
Loading: UN
>> #
>> #       Load water and ions
>> # 
>> loadOff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
>> loadOff solvents.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: MEOHBOX
Loading: NMABOX
Loading: OPC
Loading: OPCBOX
Loading: PL3
Loading: POL3BOX
Loading: QSPCFWBOX
Loading: SPC
Loading: SPCBOX
Loading: SPCFWBOX
Loading: SPF
Loading: SPG
Loading: T4E
Loading: TIP3PBOX
Loading: TIP3PFBOX
Loading: TIP4PBOX
Loading: TIP4PEWBOX
Loading: TIP5PBOX
Loading: TP3
Loading: TP4
Loading: TP5
Loading: TPF
>> HOH = TP3
>> WAT = TP3
>> 
>> #
>> #	Define the PDB name map for the amino acids and nucleic acids
>> #     (note: no NHYP!  use neutral form for now)
>> #
>> addPdbResMap {
>>   { 0 "HYP" "HYP"  } { 1 "HYP" "CHYP" }
>>   { 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
>>   { 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
>>   { 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
>>   { 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
>>   { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
>>   { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
>>   { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
>>   { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
>>   { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
>>   { 0 "HID" "NHID" } { 1 "HID" "CHID" }
>>   { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
>>   { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
>>   { 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
>>   { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
>>   { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
>>   { 0 "MET" "NMET" } { 1 "MET" "CMET" }
>>   { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
>>   { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
>>   { 0 "SER" "NSER" } { 1 "SER" "CSER" }
>>   { 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
>>   { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
>>   { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
>>   { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
>>   { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
>>   { 0 "G" "G5"  } { 1 "G" "G3"  } 
>>   { 0 "A" "A5"  } { 1 "A" "A3"  } 
>>   { 0 "C" "C5"  } { 1 "C" "C3"  } 
>>   { 0 "U" "U5"  } { 1 "U" "U3"  } 
>>   { 0 "DG" "DG5"  } { 1 "DG" "DG3"  }  
>>   { 0 "DA" "DA5"  } { 1 "DA" "DA3"  }  
>>   { 0 "DC" "DC5"  } { 1 "DC" "DC3"  }  
>>   { 0 "DT" "DT5"  } { 1 "DT" "DT3"  }  
>> #  some old Amber residue names for RNA:
>>   { 0  "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" }
>>   { 0  "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" }
>>   { 0  "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" }
>>   { 0  "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" }
>> #  some really old Amber residue names, assuming DNA:
>>   { 0 "GUA" "DG5"  } { 1 "GUA" "DG3"  } { "GUA" "DG" }
>>   { 0 "ADE" "DA5"  } { 1 "ADE" "DA3"  } { "ADE" "DA" }
>>   { 0 "CYT" "DC5"  } { 1 "CYT" "DC3"  } { "CYT" "DC" }
>>   { 0 "THY" "DT5"  } { 1 "THY" "DT3"  } { "THY" "DT" }
>> #  uncomment out the following if you have this old style RNA files:
>> # { 0 "GUA" "G5"  } { 1 "GUA" "G3"  } { "GUA" "G" }
>> # { 0 "ADE" "A5"  } { 1 "ADE" "A3"  } { "ADE" "A" }
>> # { 0 "CYT" "C5"  } { 1 "CYT" "C3"  } { "CYT" "C" }
>> # { 0 "URA" "R5"  } { 1 "URA" "R3"  } { "URA" "R" }
>> 
>> }
>> 
>> #  try to be good about reading in really old atom names as well:
>> addPdbAtomMap {
>>   { "O5*" "O5'" }
>>   { "C5*" "C5'" }
>>   { "C4*" "C4'" }
>>   { "O4*" "O4'" }
>>   { "C3*" "C3'" }
>>   { "O3*" "O3'" }
>>   { "C2*" "C2'" }
>>   { "O2*" "O2'" }
>>   { "C1*" "C1'" }
>>   { "C5M" "C7"  }
>>   { "H1*" "H1'" }
>>   { "H2*1" "H2'" }
>>   { "H2*2" "H2''" }
>>   { "HO*2" "HO2'" }
>>   { "H2'1" "H2'" }
>>   { "H2'2" "H2''" }
>>   { "H3*" "H3'" }
>>   { "H4*" "H4'" }
>>   { "H5*1" "H5'" }
>>   { "H5*2" "H5''" }
>>   { "H5'1" "H5'" }
>>   { "H5'2" "H5''" }
>>   { "HO'2" "HO2'" }
>>   { "H5T"  "HO5'" }
>>   { "H3T"  "HO3'" }
>>   { "O1'" "O4'" }
>>   { "OA"  "OP1" }
>>   { "OB"  "OP2" }
>>   { "O1P" "OP1" }
>>   { "O2P" "OP2" }
>> }
>> 
>> #
>> # assume that most often proteins use HIE
>> #
>> NHIS = NHIE
>> HIS = HIE
>> CHIS = CHIE
> 
> loadoff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
> loadamberparams frcmod.opc
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.opc
Reading force field modification type file (frcmod)
Reading title:
Parameters for OPC water (JPCL, 2014, 5 (21), pp 3863–3871) 
(UNKNOWN ATOM TYPE: EP)
> loadamberparams frcmod.ionsjc_tip4pew
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip4pew
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP4P/EW water from Joung & Cheatham JPCB (2008)
> 
> m = loadpdb init.pdb
Loading PDB file: ./init.pdb
Enter zPdbReadScan from call depth  0.
Exit  zPdbReadScan from call depth  0.
Matching PDB residue names to LEaP variables.
(Residue 0: A5, Terminal/beginning, was not found in name map.)
(Residue 1: C3, Terminal/last, was not found in name map.)
Joining A5 - C3
  total atoms in file: 63
> 
> 
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.131155 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<H4' 9>
Warning: Close contact of 1.307451 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<C4' 8>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> solvatebox m OPCBOX 10.66 iso
  Solute vdw bounding box:              12.265 11.150 10.292
  Total bounding box for atom centers:  33.585 33.585 33.585
      (box expansion for 'iso' is   9.9%)
  Solvent unit box:                     18.865 18.478 19.006
The number of boxes:  x= 2  y= 2  z= 2
Adding box at: x=0  y=0  z=0
Center of solvent box is: 9.432422, 9.239054, 9.503120
Adding box at: x=0  y=0  z=1
Center of solvent box is: 9.432422, 9.239054, -9.503120
Adding box at: x=0  y=1  z=0
Center of solvent box is: 9.432422, -9.239054, 9.503120
Adding box at: x=0  y=1  z=1
Center of solvent box is: 9.432422, -9.239054, -9.503120
Adding box at: x=1  y=0  z=0
Center of solvent box is: -9.432422, 9.239054, 9.503120
Adding box at: x=1  y=0  z=1
Center of solvent box is: -9.432422, 9.239054, -9.503120
Adding box at: x=1  y=1  z=0
Center of solvent box is: -9.432422, -9.239054, 9.503120
Adding box at: x=1  y=1  z=1
Center of solvent box is: -9.432422, -9.239054, -9.503120
  Volume: 48622.506 A^3 
  Total mass 20100.776 amu,  Density 0.686 g/cc
  Added 1084 residues.
> 
> addions m Na+ 0
1 Na+ ion required to neutralize.
Adding 1 counter ions to "m" using 1A grid
Total solute charge:  -1.00  Max atom radius:   2.10
Grid extends from solute vdw + 1.23  to  7.33
Box:
   enclosing:  -11.90 -11.84 -11.12   12.54 11.30 11.09
   sized:			      20.10 20.16 20.88
   edge:        32.00
Resolution:      1.00 Angstrom.
Tree depth: 5
grid build: 0 sec
Volume = 15.67% of box, grid points 5135
Solvent present: replacing closest with ion
	 when steric overlaps occur
Calculating grid charges
charges: 0 sec
(Replacing solvent molecule)
Placed Na+ in m at (-5.98, 4.85, -2.80).

Done adding ions.
> addions m Na+ 5 Cl- 5
Na+ has a charge of 0.
Adding the ions anyway.
Adding 10 counter ions to "m" using 1A grid
Total solute charge:   0.00  Max atom radius:   2.10
Grid extends from solute vdw + 6.14  to  12.24
Box:
   enclosing:  -18.22 -16.75 -16.03   17.46 17.09 16.00
   sized:			      45.78 47.25 47.97
   edge:        64.00
Resolution:      1.00 Angstrom.
Tree depth: 6
grid build: 0 sec
Volume =  4.90% of box, grid points 12839
Solvent present: replacing closest with ion
	 when steric overlaps occur
Calculating grid charges
charges: 0 sec
(Replacing solvent molecule)
Placed Na+ in m at (-0.14, -3.24, 9.75).
(Replacing solvent molecule)
Placed Cl- in m at (2.85, -0.94, 8.58).
(Replacing solvent molecule)
Placed Na+ in m at (8.07, 1.13, 7.86).
(Replacing solvent molecule)
Placed Cl- in m at (-0.46, 0.47, 14.00).
(Replacing solvent molecule)
Placed Na+ in m at (3.98, 1.37, 9.85).
(Replacing solvent molecule)
Placed Cl- in m at (8.42, 0.74, 10.66).
(Replacing solvent molecule)
Placed Na+ in m at (1.80, 4.34, 13.61).
(Replacing solvent molecule)
Placed Cl- in m at (4.87, 5.75, 10.61).
(Replacing solvent molecule)
Placed Na+ in m at (7.00, 4.40, 11.69).
(Replacing solvent molecule)
Placed Cl- in m at (3.61, 1.91, 13.32).

Done adding ions.
> 
> saveamberparm m full.topo non-randomized.crds
Checking Unit.

 -- ignoring the warnings.

Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 ** Warning: No sp2 improper torsion term for  N*-CB-CB-NC
        atoms are: N9 C5 C4 N3
 ** Warning: No sp2 improper torsion term for  NB-CA-CB-CB
        atoms are: N7 C6 C5 C4
 total 11 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
 (no restraints)
> quit
	Quit
log started: Sun Nov  1 20:52:17 2015

Log file: ./leap.log
>> #
>> # ----- leaprc for loading the ff12SB force field
>> # ----- NOTE: this is designed for PDB format 3!
>> #    Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA
>> #
>> #	load atom type hybridizations
>> #
>> addAtomTypes {
>> 	{ "H"   "H" "sp3" }
>> 	{ "HO"  "H" "sp3" }
>> 	{ "HS"  "H" "sp3" }
>> 	{ "H1"  "H" "sp3" }
>> 	{ "H2"  "H" "sp3" }
>> 	{ "H3"  "H" "sp3" }
>> 	{ "H4"  "H" "sp3" }
>> 	{ "H5"  "H" "sp3" }
>> 	{ "HW"  "H" "sp3" }
>> 	{ "HC"  "H" "sp3" }
>> 	{ "HA"  "H" "sp3" }
>> 	{ "HP"  "H" "sp3" }
>> 	{ "HZ"  "H" "sp3" }
>> 	{ "OH"  "O" "sp3" }
>> 	{ "OS"  "O" "sp3" }
>> 	{ "O"   "O" "sp2" }
>> 	{ "O2"  "O" "sp2" }
>> 	{ "OP"  "O" "sp2" }
>> 	{ "OW"  "O" "sp3" }
>> 	{ "CT"  "C" "sp3" }
>> 	{ "CX"  "C" "sp3" }
>> 	{ "C8"  "C" "sp3" }
>> 	{ "2C"  "C" "sp3" }
>> 	{ "3C"  "C" "sp3" }
>> 	{ "CH"  "C" "sp3" }
>> 	{ "CS"  "C" "sp2" }
>> 	{ "C"   "C" "sp2" }
>> 	{ "CO"   "C" "sp2" }
>> 	{ "C*"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CB"  "C" "sp2" }
>> 	{ "CC"  "C" "sp2" }
>> 	{ "CN"  "C" "sp2" }
>> 	{ "CM"  "C" "sp2" }
>> 	{ "CK"  "C" "sp2" }
>> 	{ "CQ"  "C" "sp2" }
>> 	{ "CD"  "C" "sp2" }
>> 	{ "C5"  "C" "sp2" }
>> 	{ "C4"  "C" "sp2" }
>> 	{ "CP"  "C" "sp2" }
>> 	{ "CI"  "C" "sp3" }
>> 	{ "CJ"  "C" "sp2" }
>> 	{ "CW"  "C" "sp2" }
>> 	{ "CV"  "C" "sp2" }
>> 	{ "CR"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CY"  "C" "sp2" }
>> 	{ "C0"  "Ca" "sp3" }
>> 	{ "MG"  "Mg" "sp3" }
>> 	{ "N"   "N" "sp2" }
>> 	{ "NA"  "N" "sp2" }
>> 	{ "N2"  "N" "sp2" }
>> 	{ "N*"  "N" "sp2" }
>> 	{ "NP"  "N" "sp2" }
>> 	{ "NQ"  "N" "sp2" }
>> 	{ "NB"  "N" "sp2" }
>> 	{ "NC"  "N" "sp2" }
>> 	{ "NT"  "N" "sp3" }
>> 	{ "NY"  "N" "sp2" }
>> 	{ "N3"  "N" "sp3" }
>> 	{ "S"   "S" "sp3" }
>> 	{ "SH"  "S" "sp3" }
>> 	{ "P"   "P" "sp3" }
>> 	{ "LP"  ""  "sp3" }
>> 	{ "EP"  ""  "sp3" }
>> 	{ "F"   "F" "sp3" }
>> 	{ "Cl"  "Cl" "sp3" }
>> 	{ "Br"  "Br" "sp3" }
>> 	{ "I"   "I"  "sp3" }
>> 	{ "F-"   "F" "sp3" }
>> 	{ "Cl-"  "Cl" "sp3" }
>> 	{ "Br-"  "Br" "sp3" }
>> 	{ "I-"   "I"  "sp3" }
>> 	{ "Li+"  "Li"  "sp3" }
>> 	{ "Na+"  "Na"  "sp3" }
>> 	{ "K+"  "K"  "sp3" }
>> 	{ "Rb+"  "Rb"  "sp3" }
>> 	{ "Cs+"  "Cs"  "sp3" }
>> 	{ "Mg+"  "Mg"  "sp3" }
>> # glycam
>> 	{ "OG"  "O" "sp3" }
>> 	{ "OL"  "O" "sp3" }
>> 	{ "AC"  "C" "sp3" }
>> 	{ "EC"  "C" "sp3" }
>> }
>> #
>> #	Load the main parameter set.
>> #
>> parm10 = loadamberparams parm10.dat
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
(UNKNOWN ATOM TYPE: Zn)
(UNKNOWN ATOM TYPE: EP)
>> frcmod12SB = loadamberparams frcmod.ff12SB
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff12SB
Reading force field modification type file (frcmod)
Reading title:
ff12SB protein backbone and sidechain parameters
>> #
>> #	Load main chain and terminating amino acid libraries, nucleic acids
>> #
>> loadOff amino12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/amino12.lib
Loading: ALA
Loading: ARG
Loading: ASH
Loading: ASN
Loading: ASP
Loading: CYM
Loading: CYS
Loading: CYX
Loading: GLH
Loading: GLN
Loading: GLU
Loading: GLY
Loading: HID
Loading: HIE
Loading: HIP
Loading: HYP
Loading: ILE
Loading: LEU
Loading: LYN
Loading: LYS
Loading: MET
Loading: PHE
Loading: PRO
Loading: SER
Loading: THR
Loading: TRP
Loading: TYR
Loading: VAL
>> loadOff aminoct12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminoct12.lib
Loading: CALA
Loading: CARG
Loading: CASN
Loading: CASP
Loading: CCYS
Loading: CCYX
Loading: CGLN
Loading: CGLU
Loading: CGLY
Loading: CHID
Loading: CHIE
Loading: CHIP
Loading: CHYP
Loading: CILE
Loading: CLEU
Loading: CLYS
Loading: CMET
Loading: CPHE
Loading: CPRO
Loading: CSER
Loading: CTHR
Loading: CTRP
Loading: CTYR
Loading: CVAL
Loading: NHE
Loading: NME
>> loadOff aminont12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminont12.lib
Loading: ACE
Loading: NALA
Loading: NARG
Loading: NASN
Loading: NASP
Loading: NCYS
Loading: NCYX
Loading: NGLN
Loading: NGLU
Loading: NGLY
Loading: NHID
Loading: NHIE
Loading: NHIP
Loading: NILE
Loading: NLEU
Loading: NLYS
Loading: NMET
Loading: NPHE
Loading: NPRO
Loading: NSER
Loading: NTHR
Loading: NTRP
Loading: NTYR
Loading: NVAL
>> loadOff nucleic12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/nucleic12.lib
Loading: A
Loading: A3
Loading: A5
Loading: AN
Loading: C
Loading: C3
Loading: C5
Loading: CN
Loading: DA
Loading: DA3
Loading: DA5
Loading: DAN
Loading: DC
Loading: DC3
Loading: DC5
Loading: DCN
Loading: DG
Loading: DG3
Loading: DG5
Loading: DGN
Loading: DT
Loading: DT3
Loading: DT5
Loading: DTN
Loading: G
Loading: G3
Loading: G5
Loading: GN
Loading: OHE
Loading: U
Loading: U3
Loading: U5
Loading: UN
>> #
>> #       Load water and ions
>> # 
>> loadOff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
>> loadOff solvents.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: MEOHBOX
Loading: NMABOX
Loading: OPC
Loading: OPCBOX
Loading: PL3
Loading: POL3BOX
Loading: QSPCFWBOX
Loading: SPC
Loading: SPCBOX
Loading: SPCFWBOX
Loading: SPF
Loading: SPG
Loading: T4E
Loading: TIP3PBOX
Loading: TIP3PFBOX
Loading: TIP4PBOX
Loading: TIP4PEWBOX
Loading: TIP5PBOX
Loading: TP3
Loading: TP4
Loading: TP5
Loading: TPF
>> HOH = TP3
>> WAT = TP3
>> 
>> #
>> #	Define the PDB name map for the amino acids and nucleic acids
>> #     (note: no NHYP!  use neutral form for now)
>> #
>> addPdbResMap {
>>   { 0 "HYP" "HYP"  } { 1 "HYP" "CHYP" }
>>   { 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
>>   { 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
>>   { 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
>>   { 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
>>   { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
>>   { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
>>   { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
>>   { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
>>   { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
>>   { 0 "HID" "NHID" } { 1 "HID" "CHID" }
>>   { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
>>   { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
>>   { 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
>>   { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
>>   { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
>>   { 0 "MET" "NMET" } { 1 "MET" "CMET" }
>>   { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
>>   { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
>>   { 0 "SER" "NSER" } { 1 "SER" "CSER" }
>>   { 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
>>   { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
>>   { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
>>   { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
>>   { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
>>   { 0 "G" "G5"  } { 1 "G" "G3"  } 
>>   { 0 "A" "A5"  } { 1 "A" "A3"  } 
>>   { 0 "C" "C5"  } { 1 "C" "C3"  } 
>>   { 0 "U" "U5"  } { 1 "U" "U3"  } 
>>   { 0 "DG" "DG5"  } { 1 "DG" "DG3"  }  
>>   { 0 "DA" "DA5"  } { 1 "DA" "DA3"  }  
>>   { 0 "DC" "DC5"  } { 1 "DC" "DC3"  }  
>>   { 0 "DT" "DT5"  } { 1 "DT" "DT3"  }  
>> #  some old Amber residue names for RNA:
>>   { 0  "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" }
>>   { 0  "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" }
>>   { 0  "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" }
>>   { 0  "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" }
>> #  some really old Amber residue names, assuming DNA:
>>   { 0 "GUA" "DG5"  } { 1 "GUA" "DG3"  } { "GUA" "DG" }
>>   { 0 "ADE" "DA5"  } { 1 "ADE" "DA3"  } { "ADE" "DA" }
>>   { 0 "CYT" "DC5"  } { 1 "CYT" "DC3"  } { "CYT" "DC" }
>>   { 0 "THY" "DT5"  } { 1 "THY" "DT3"  } { "THY" "DT" }
>> #  uncomment out the following if you have this old style RNA files:
>> # { 0 "GUA" "G5"  } { 1 "GUA" "G3"  } { "GUA" "G" }
>> # { 0 "ADE" "A5"  } { 1 "ADE" "A3"  } { "ADE" "A" }
>> # { 0 "CYT" "C5"  } { 1 "CYT" "C3"  } { "CYT" "C" }
>> # { 0 "URA" "R5"  } { 1 "URA" "R3"  } { "URA" "R" }
>> 
>> }
>> 
>> #  try to be good about reading in really old atom names as well:
>> addPdbAtomMap {
>>   { "O5*" "O5'" }
>>   { "C5*" "C5'" }
>>   { "C4*" "C4'" }
>>   { "O4*" "O4'" }
>>   { "C3*" "C3'" }
>>   { "O3*" "O3'" }
>>   { "C2*" "C2'" }
>>   { "O2*" "O2'" }
>>   { "C1*" "C1'" }
>>   { "C5M" "C7"  }
>>   { "H1*" "H1'" }
>>   { "H2*1" "H2'" }
>>   { "H2*2" "H2''" }
>>   { "HO*2" "HO2'" }
>>   { "H2'1" "H2'" }
>>   { "H2'2" "H2''" }
>>   { "H3*" "H3'" }
>>   { "H4*" "H4'" }
>>   { "H5*1" "H5'" }
>>   { "H5*2" "H5''" }
>>   { "H5'1" "H5'" }
>>   { "H5'2" "H5''" }
>>   { "HO'2" "HO2'" }
>>   { "H5T"  "HO5'" }
>>   { "H3T"  "HO3'" }
>>   { "O1'" "O4'" }
>>   { "OA"  "OP1" }
>>   { "OB"  "OP2" }
>>   { "O1P" "OP1" }
>>   { "O2P" "OP2" }
>> }
>> 
>> #
>> # assume that most often proteins use HIE
>> #
>> NHIS = NHIE
>> HIS = HIE
>> CHIS = CHIE
> 
> loadoff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
> loadamberparams frcmod.opc
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.opc
Reading force field modification type file (frcmod)
Reading title:
Parameters for OPC water (JPCL, 2014, 5 (21), pp 3863–3871) 
(UNKNOWN ATOM TYPE: EP)
> loadamberparams frcmod.ionsjc_tip4pew
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip4pew
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP4P/EW water from Joung & Cheatham JPCB (2008)
> 
> m = loadpdb init.pdb
Loading PDB file: ./init.pdb
Enter zPdbReadScan from call depth  0.
Exit  zPdbReadScan from call depth  0.
Matching PDB residue names to LEaP variables.
(Residue 0: A5, Terminal/beginning, was not found in name map.)
(Residue 1: C3, Terminal/last, was not found in name map.)
Joining A5 - C3
  total atoms in file: 63
> 
> 
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.131155 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<H4' 9>
Warning: Close contact of 1.307451 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<C4' 8>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> solvatebox m OPCBOX 10.66 iso
  Solute vdw bounding box:              12.265 11.150 10.292
  Total bounding box for atom centers:  33.585 33.585 33.585
      (box expansion for 'iso' is   9.9%)
  Solvent unit box:                     18.865 18.478 19.006
The number of boxes:  x= 2  y= 2  z= 2
Adding box at: x=0  y=0  z=0
Center of solvent box is: 9.432422, 9.239054, 9.503120
Adding box at: x=0  y=0  z=1
Center of solvent box is: 9.432422, 9.239054, -9.503120
Adding box at: x=0  y=1  z=0
Center of solvent box is: 9.432422, -9.239054, 9.503120
Adding box at: x=0  y=1  z=1
Center of solvent box is: 9.432422, -9.239054, -9.503120
Adding box at: x=1  y=0  z=0
Center of solvent box is: -9.432422, 9.239054, 9.503120
Adding box at: x=1  y=0  z=1
Center of solvent box is: -9.432422, 9.239054, -9.503120
Adding box at: x=1  y=1  z=0
Center of solvent box is: -9.432422, -9.239054, 9.503120
Adding box at: x=1  y=1  z=1
Center of solvent box is: -9.432422, -9.239054, -9.503120
  Volume: 48622.506 A^3 
  Total mass 20100.776 amu,  Density 0.686 g/cc
  Added 1084 residues.
> 
> addions m Na+ 0
1 Na+ ion required to neutralize.
Adding 1 counter ions to "m" using 1A grid
Total solute charge:  -1.00  Max atom radius:   2.10
Grid extends from solute vdw + 1.23  to  7.33
Box:
   enclosing:  -11.90 -11.84 -11.12   12.54 11.30 11.09
   sized:			      20.10 20.16 20.88
   edge:        32.00
Resolution:      1.00 Angstrom.
Tree depth: 5
grid build: 0 sec
Volume = 15.67% of box, grid points 5135
Solvent present: replacing closest with ion
	 when steric overlaps occur
Calculating grid charges
charges: 0 sec
(Replacing solvent molecule)
Placed Na+ in m at (-5.98, 4.85, -2.80).

Done adding ions.
> addions m Na+ 5 Cl- 5
Na+ has a charge of 0.
Adding the ions anyway.
Adding 10 counter ions to "m" using 1A grid
Total solute charge:   0.00  Max atom radius:   2.10
Grid extends from solute vdw + 6.14  to  12.24
Box:
   enclosing:  -18.22 -16.75 -16.03   17.46 17.09 16.00
   sized:			      45.78 47.25 47.97
   edge:        64.00
Resolution:      1.00 Angstrom.
Tree depth: 6
grid build: 0 sec
Volume =  4.90% of box, grid points 12839
Solvent present: replacing closest with ion
	 when steric overlaps occur
Calculating grid charges
charges: 0 sec
(Replacing solvent molecule)
Placed Na+ in m at (-0.14, -3.24, 9.75).
(Replacing solvent molecule)
Placed Cl- in m at (2.85, -0.94, 8.58).
(Replacing solvent molecule)
Placed Na+ in m at (8.07, 1.13, 7.86).
(Replacing solvent molecule)
Placed Cl- in m at (-0.46, 0.47, 14.00).
(Replacing solvent molecule)
Placed Na+ in m at (3.98, 1.37, 9.85).
(Replacing solvent molecule)
Placed Cl- in m at (8.42, 0.74, 10.66).
(Replacing solvent molecule)
Placed Na+ in m at (1.80, 4.34, 13.61).
(Replacing solvent molecule)
Placed Cl- in m at (4.87, 5.75, 10.61).
(Replacing solvent molecule)
Placed Na+ in m at (7.00, 4.40, 11.69).
(Replacing solvent molecule)
Placed Cl- in m at (3.61, 1.91, 13.32).

Done adding ions.
> 
> saveamberparm m full.topo non-randomized.crds
Checking Unit.

 -- ignoring the warnings.

Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 ** Warning: No sp2 improper torsion term for  N*-CB-CB-NC
        atoms are: N9 C5 C4 N3
 ** Warning: No sp2 improper torsion term for  NB-CA-CB-CB
        atoms are: N7 C6 C5 C4
 total 11 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
 (no restraints)
> quit
	Quit
log started: Sun Nov  1 20:53:01 2015

Log file: ./leap.log
>> #
>> # ----- leaprc for loading the ff12SB force field
>> # ----- NOTE: this is designed for PDB format 3!
>> #    Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA
>> #
>> #	load atom type hybridizations
>> #
>> addAtomTypes {
>> 	{ "H"   "H" "sp3" }
>> 	{ "HO"  "H" "sp3" }
>> 	{ "HS"  "H" "sp3" }
>> 	{ "H1"  "H" "sp3" }
>> 	{ "H2"  "H" "sp3" }
>> 	{ "H3"  "H" "sp3" }
>> 	{ "H4"  "H" "sp3" }
>> 	{ "H5"  "H" "sp3" }
>> 	{ "HW"  "H" "sp3" }
>> 	{ "HC"  "H" "sp3" }
>> 	{ "HA"  "H" "sp3" }
>> 	{ "HP"  "H" "sp3" }
>> 	{ "HZ"  "H" "sp3" }
>> 	{ "OH"  "O" "sp3" }
>> 	{ "OS"  "O" "sp3" }
>> 	{ "O"   "O" "sp2" }
>> 	{ "O2"  "O" "sp2" }
>> 	{ "OP"  "O" "sp2" }
>> 	{ "OW"  "O" "sp3" }
>> 	{ "CT"  "C" "sp3" }
>> 	{ "CX"  "C" "sp3" }
>> 	{ "C8"  "C" "sp3" }
>> 	{ "2C"  "C" "sp3" }
>> 	{ "3C"  "C" "sp3" }
>> 	{ "CH"  "C" "sp3" }
>> 	{ "CS"  "C" "sp2" }
>> 	{ "C"   "C" "sp2" }
>> 	{ "CO"   "C" "sp2" }
>> 	{ "C*"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CB"  "C" "sp2" }
>> 	{ "CC"  "C" "sp2" }
>> 	{ "CN"  "C" "sp2" }
>> 	{ "CM"  "C" "sp2" }
>> 	{ "CK"  "C" "sp2" }
>> 	{ "CQ"  "C" "sp2" }
>> 	{ "CD"  "C" "sp2" }
>> 	{ "C5"  "C" "sp2" }
>> 	{ "C4"  "C" "sp2" }
>> 	{ "CP"  "C" "sp2" }
>> 	{ "CI"  "C" "sp3" }
>> 	{ "CJ"  "C" "sp2" }
>> 	{ "CW"  "C" "sp2" }
>> 	{ "CV"  "C" "sp2" }
>> 	{ "CR"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CY"  "C" "sp2" }
>> 	{ "C0"  "Ca" "sp3" }
>> 	{ "MG"  "Mg" "sp3" }
>> 	{ "N"   "N" "sp2" }
>> 	{ "NA"  "N" "sp2" }
>> 	{ "N2"  "N" "sp2" }
>> 	{ "N*"  "N" "sp2" }
>> 	{ "NP"  "N" "sp2" }
>> 	{ "NQ"  "N" "sp2" }
>> 	{ "NB"  "N" "sp2" }
>> 	{ "NC"  "N" "sp2" }
>> 	{ "NT"  "N" "sp3" }
>> 	{ "NY"  "N" "sp2" }
>> 	{ "N3"  "N" "sp3" }
>> 	{ "S"   "S" "sp3" }
>> 	{ "SH"  "S" "sp3" }
>> 	{ "P"   "P" "sp3" }
>> 	{ "LP"  ""  "sp3" }
>> 	{ "EP"  ""  "sp3" }
>> 	{ "F"   "F" "sp3" }
>> 	{ "Cl"  "Cl" "sp3" }
>> 	{ "Br"  "Br" "sp3" }
>> 	{ "I"   "I"  "sp3" }
>> 	{ "F-"   "F" "sp3" }
>> 	{ "Cl-"  "Cl" "sp3" }
>> 	{ "Br-"  "Br" "sp3" }
>> 	{ "I-"   "I"  "sp3" }
>> 	{ "Li+"  "Li"  "sp3" }
>> 	{ "Na+"  "Na"  "sp3" }
>> 	{ "K+"  "K"  "sp3" }
>> 	{ "Rb+"  "Rb"  "sp3" }
>> 	{ "Cs+"  "Cs"  "sp3" }
>> 	{ "Mg+"  "Mg"  "sp3" }
>> # glycam
>> 	{ "OG"  "O" "sp3" }
>> 	{ "OL"  "O" "sp3" }
>> 	{ "AC"  "C" "sp3" }
>> 	{ "EC"  "C" "sp3" }
>> }
>> #
>> #	Load the main parameter set.
>> #
>> parm10 = loadamberparams parm10.dat
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
(UNKNOWN ATOM TYPE: Zn)
(UNKNOWN ATOM TYPE: EP)
>> frcmod12SB = loadamberparams frcmod.ff12SB
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff12SB
Reading force field modification type file (frcmod)
Reading title:
ff12SB protein backbone and sidechain parameters
>> #
>> #	Load main chain and terminating amino acid libraries, nucleic acids
>> #
>> loadOff amino12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/amino12.lib
Loading: ALA
Loading: ARG
Loading: ASH
Loading: ASN
Loading: ASP
Loading: CYM
Loading: CYS
Loading: CYX
Loading: GLH
Loading: GLN
Loading: GLU
Loading: GLY
Loading: HID
Loading: HIE
Loading: HIP
Loading: HYP
Loading: ILE
Loading: LEU
Loading: LYN
Loading: LYS
Loading: MET
Loading: PHE
Loading: PRO
Loading: SER
Loading: THR
Loading: TRP
Loading: TYR
Loading: VAL
>> loadOff aminoct12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminoct12.lib
Loading: CALA
Loading: CARG
Loading: CASN
Loading: CASP
Loading: CCYS
Loading: CCYX
Loading: CGLN
Loading: CGLU
Loading: CGLY
Loading: CHID
Loading: CHIE
Loading: CHIP
Loading: CHYP
Loading: CILE
Loading: CLEU
Loading: CLYS
Loading: CMET
Loading: CPHE
Loading: CPRO
Loading: CSER
Loading: CTHR
Loading: CTRP
Loading: CTYR
Loading: CVAL
Loading: NHE
Loading: NME
>> loadOff aminont12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminont12.lib
Loading: ACE
Loading: NALA
Loading: NARG
Loading: NASN
Loading: NASP
Loading: NCYS
Loading: NCYX
Loading: NGLN
Loading: NGLU
Loading: NGLY
Loading: NHID
Loading: NHIE
Loading: NHIP
Loading: NILE
Loading: NLEU
Loading: NLYS
Loading: NMET
Loading: NPHE
Loading: NPRO
Loading: NSER
Loading: NTHR
Loading: NTRP
Loading: NTYR
Loading: NVAL
>> loadOff nucleic12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/nucleic12.lib
Loading: A
Loading: A3
Loading: A5
Loading: AN
Loading: C
Loading: C3
Loading: C5
Loading: CN
Loading: DA
Loading: DA3
Loading: DA5
Loading: DAN
Loading: DC
Loading: DC3
Loading: DC5
Loading: DCN
Loading: DG
Loading: DG3
Loading: DG5
Loading: DGN
Loading: DT
Loading: DT3
Loading: DT5
Loading: DTN
Loading: G
Loading: G3
Loading: G5
Loading: GN
Loading: OHE
Loading: U
Loading: U3
Loading: U5
Loading: UN
>> #
>> #       Load water and ions
>> # 
>> loadOff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
>> loadOff solvents.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: MEOHBOX
Loading: NMABOX
Loading: OPC
Loading: OPCBOX
Loading: PL3
Loading: POL3BOX
Loading: QSPCFWBOX
Loading: SPC
Loading: SPCBOX
Loading: SPCFWBOX
Loading: SPF
Loading: SPG
Loading: T4E
Loading: TIP3PBOX
Loading: TIP3PFBOX
Loading: TIP4PBOX
Loading: TIP4PEWBOX
Loading: TIP5PBOX
Loading: TP3
Loading: TP4
Loading: TP5
Loading: TPF
>> HOH = TP3
>> WAT = TP3
>> 
>> #
>> #	Define the PDB name map for the amino acids and nucleic acids
>> #     (note: no NHYP!  use neutral form for now)
>> #
>> addPdbResMap {
>>   { 0 "HYP" "HYP"  } { 1 "HYP" "CHYP" }
>>   { 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
>>   { 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
>>   { 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
>>   { 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
>>   { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
>>   { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
>>   { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
>>   { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
>>   { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
>>   { 0 "HID" "NHID" } { 1 "HID" "CHID" }
>>   { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
>>   { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
>>   { 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
>>   { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
>>   { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
>>   { 0 "MET" "NMET" } { 1 "MET" "CMET" }
>>   { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
>>   { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
>>   { 0 "SER" "NSER" } { 1 "SER" "CSER" }
>>   { 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
>>   { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
>>   { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
>>   { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
>>   { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
>>   { 0 "G" "G5"  } { 1 "G" "G3"  } 
>>   { 0 "A" "A5"  } { 1 "A" "A3"  } 
>>   { 0 "C" "C5"  } { 1 "C" "C3"  } 
>>   { 0 "U" "U5"  } { 1 "U" "U3"  } 
>>   { 0 "DG" "DG5"  } { 1 "DG" "DG3"  }  
>>   { 0 "DA" "DA5"  } { 1 "DA" "DA3"  }  
>>   { 0 "DC" "DC5"  } { 1 "DC" "DC3"  }  
>>   { 0 "DT" "DT5"  } { 1 "DT" "DT3"  }  
>> #  some old Amber residue names for RNA:
>>   { 0  "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" }
>>   { 0  "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" }
>>   { 0  "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" }
>>   { 0  "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" }
>> #  some really old Amber residue names, assuming DNA:
>>   { 0 "GUA" "DG5"  } { 1 "GUA" "DG3"  } { "GUA" "DG" }
>>   { 0 "ADE" "DA5"  } { 1 "ADE" "DA3"  } { "ADE" "DA" }
>>   { 0 "CYT" "DC5"  } { 1 "CYT" "DC3"  } { "CYT" "DC" }
>>   { 0 "THY" "DT5"  } { 1 "THY" "DT3"  } { "THY" "DT" }
>> #  uncomment out the following if you have this old style RNA files:
>> # { 0 "GUA" "G5"  } { 1 "GUA" "G3"  } { "GUA" "G" }
>> # { 0 "ADE" "A5"  } { 1 "ADE" "A3"  } { "ADE" "A" }
>> # { 0 "CYT" "C5"  } { 1 "CYT" "C3"  } { "CYT" "C" }
>> # { 0 "URA" "R5"  } { 1 "URA" "R3"  } { "URA" "R" }
>> 
>> }
>> 
>> #  try to be good about reading in really old atom names as well:
>> addPdbAtomMap {
>>   { "O5*" "O5'" }
>>   { "C5*" "C5'" }
>>   { "C4*" "C4'" }
>>   { "O4*" "O4'" }
>>   { "C3*" "C3'" }
>>   { "O3*" "O3'" }
>>   { "C2*" "C2'" }
>>   { "O2*" "O2'" }
>>   { "C1*" "C1'" }
>>   { "C5M" "C7"  }
>>   { "H1*" "H1'" }
>>   { "H2*1" "H2'" }
>>   { "H2*2" "H2''" }
>>   { "HO*2" "HO2'" }
>>   { "H2'1" "H2'" }
>>   { "H2'2" "H2''" }
>>   { "H3*" "H3'" }
>>   { "H4*" "H4'" }
>>   { "H5*1" "H5'" }
>>   { "H5*2" "H5''" }
>>   { "H5'1" "H5'" }
>>   { "H5'2" "H5''" }
>>   { "HO'2" "HO2'" }
>>   { "H5T"  "HO5'" }
>>   { "H3T"  "HO3'" }
>>   { "O1'" "O4'" }
>>   { "OA"  "OP1" }
>>   { "OB"  "OP2" }
>>   { "O1P" "OP1" }
>>   { "O2P" "OP2" }
>> }
>> 
>> #
>> # assume that most often proteins use HIE
>> #
>> NHIS = NHIE
>> HIS = HIE
>> CHIS = CHIE
> 
> loadoff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
> loadamberparams frcmod.opc
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.opc
Reading force field modification type file (frcmod)
Reading title:
Parameters for OPC water (JPCL, 2014, 5 (21), pp 3863–3871) 
(UNKNOWN ATOM TYPE: EP)
> loadamberparams frcmod.ionsjc_tip4pew
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip4pew
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP4P/EW water from Joung & Cheatham JPCB (2008)
> 
> m = loadpdb init.pdb
Loading PDB file: ./init.pdb
Enter zPdbReadScan from call depth  0.
Exit  zPdbReadScan from call depth  0.
Matching PDB residue names to LEaP variables.
(Residue 0: A5, Terminal/beginning, was not found in name map.)
(Residue 1: C3, Terminal/last, was not found in name map.)
Joining A5 - C3
  total atoms in file: 63
> 
> 
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.131155 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<H4' 9>
Warning: Close contact of 1.307451 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<C4' 8>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> solvatebox m OPCBOX 8 iso
  Solute vdw bounding box:              12.265 11.150 10.292
  Total bounding box for atom centers:  28.265 28.265 28.265
      (box expansion for 'iso' is  11.9%)
  Solvent unit box:                     18.865 18.478 19.006
The number of boxes:  x= 2  y= 2  z= 2
Adding box at: x=0  y=0  z=0
Center of solvent box is: 9.432422, 9.239054, 9.503120
Adding box at: x=0  y=0  z=1
Center of solvent box is: 9.432422, 9.239054, -9.503120
Adding box at: x=0  y=1  z=0
Center of solvent box is: 9.432422, -9.239054, 9.503120
Adding box at: x=0  y=1  z=1
Center of solvent box is: 9.432422, -9.239054, -9.503120
Adding box at: x=1  y=0  z=0
Center of solvent box is: -9.432422, 9.239054, 9.503120
Adding box at: x=1  y=0  z=1
Center of solvent box is: -9.432422, 9.239054, -9.503120
Adding box at: x=1  y=1  z=0
Center of solvent box is: -9.432422, -9.239054, 9.503120
Adding box at: x=1  y=1  z=1
Center of solvent box is: -9.432422, -9.239054, -9.503120
  Volume: 31065.671 A^3 
  Total mass 11669.288 amu,  Density 0.624 g/cc
  Added 616 residues.
> quit
	Quit
log started: Sun Nov  1 20:53:02 2015

Log file: ./leap.log
>> #
>> # ----- leaprc for loading the ff12SB force field
>> # ----- NOTE: this is designed for PDB format 3!
>> #    Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA
>> #
>> #	load atom type hybridizations
>> #
>> addAtomTypes {
>> 	{ "H"   "H" "sp3" }
>> 	{ "HO"  "H" "sp3" }
>> 	{ "HS"  "H" "sp3" }
>> 	{ "H1"  "H" "sp3" }
>> 	{ "H2"  "H" "sp3" }
>> 	{ "H3"  "H" "sp3" }
>> 	{ "H4"  "H" "sp3" }
>> 	{ "H5"  "H" "sp3" }
>> 	{ "HW"  "H" "sp3" }
>> 	{ "HC"  "H" "sp3" }
>> 	{ "HA"  "H" "sp3" }
>> 	{ "HP"  "H" "sp3" }
>> 	{ "HZ"  "H" "sp3" }
>> 	{ "OH"  "O" "sp3" }
>> 	{ "OS"  "O" "sp3" }
>> 	{ "O"   "O" "sp2" }
>> 	{ "O2"  "O" "sp2" }
>> 	{ "OP"  "O" "sp2" }
>> 	{ "OW"  "O" "sp3" }
>> 	{ "CT"  "C" "sp3" }
>> 	{ "CX"  "C" "sp3" }
>> 	{ "C8"  "C" "sp3" }
>> 	{ "2C"  "C" "sp3" }
>> 	{ "3C"  "C" "sp3" }
>> 	{ "CH"  "C" "sp3" }
>> 	{ "CS"  "C" "sp2" }
>> 	{ "C"   "C" "sp2" }
>> 	{ "CO"   "C" "sp2" }
>> 	{ "C*"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CB"  "C" "sp2" }
>> 	{ "CC"  "C" "sp2" }
>> 	{ "CN"  "C" "sp2" }
>> 	{ "CM"  "C" "sp2" }
>> 	{ "CK"  "C" "sp2" }
>> 	{ "CQ"  "C" "sp2" }
>> 	{ "CD"  "C" "sp2" }
>> 	{ "C5"  "C" "sp2" }
>> 	{ "C4"  "C" "sp2" }
>> 	{ "CP"  "C" "sp2" }
>> 	{ "CI"  "C" "sp3" }
>> 	{ "CJ"  "C" "sp2" }
>> 	{ "CW"  "C" "sp2" }
>> 	{ "CV"  "C" "sp2" }
>> 	{ "CR"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CY"  "C" "sp2" }
>> 	{ "C0"  "Ca" "sp3" }
>> 	{ "MG"  "Mg" "sp3" }
>> 	{ "N"   "N" "sp2" }
>> 	{ "NA"  "N" "sp2" }
>> 	{ "N2"  "N" "sp2" }
>> 	{ "N*"  "N" "sp2" }
>> 	{ "NP"  "N" "sp2" }
>> 	{ "NQ"  "N" "sp2" }
>> 	{ "NB"  "N" "sp2" }
>> 	{ "NC"  "N" "sp2" }
>> 	{ "NT"  "N" "sp3" }
>> 	{ "NY"  "N" "sp2" }
>> 	{ "N3"  "N" "sp3" }
>> 	{ "S"   "S" "sp3" }
>> 	{ "SH"  "S" "sp3" }
>> 	{ "P"   "P" "sp3" }
>> 	{ "LP"  ""  "sp3" }
>> 	{ "EP"  ""  "sp3" }
>> 	{ "F"   "F" "sp3" }
>> 	{ "Cl"  "Cl" "sp3" }
>> 	{ "Br"  "Br" "sp3" }
>> 	{ "I"   "I"  "sp3" }
>> 	{ "F-"   "F" "sp3" }
>> 	{ "Cl-"  "Cl" "sp3" }
>> 	{ "Br-"  "Br" "sp3" }
>> 	{ "I-"   "I"  "sp3" }
>> 	{ "Li+"  "Li"  "sp3" }
>> 	{ "Na+"  "Na"  "sp3" }
>> 	{ "K+"  "K"  "sp3" }
>> 	{ "Rb+"  "Rb"  "sp3" }
>> 	{ "Cs+"  "Cs"  "sp3" }
>> 	{ "Mg+"  "Mg"  "sp3" }
>> # glycam
>> 	{ "OG"  "O" "sp3" }
>> 	{ "OL"  "O" "sp3" }
>> 	{ "AC"  "C" "sp3" }
>> 	{ "EC"  "C" "sp3" }
>> }
>> #
>> #	Load the main parameter set.
>> #
>> parm10 = loadamberparams parm10.dat
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
(UNKNOWN ATOM TYPE: Zn)
(UNKNOWN ATOM TYPE: EP)
>> frcmod12SB = loadamberparams frcmod.ff12SB
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff12SB
Reading force field modification type file (frcmod)
Reading title:
ff12SB protein backbone and sidechain parameters
>> #
>> #	Load main chain and terminating amino acid libraries, nucleic acids
>> #
>> loadOff amino12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/amino12.lib
Loading: ALA
Loading: ARG
Loading: ASH
Loading: ASN
Loading: ASP
Loading: CYM
Loading: CYS
Loading: CYX
Loading: GLH
Loading: GLN
Loading: GLU
Loading: GLY
Loading: HID
Loading: HIE
Loading: HIP
Loading: HYP
Loading: ILE
Loading: LEU
Loading: LYN
Loading: LYS
Loading: MET
Loading: PHE
Loading: PRO
Loading: SER
Loading: THR
Loading: TRP
Loading: TYR
Loading: VAL
>> loadOff aminoct12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminoct12.lib
Loading: CALA
Loading: CARG
Loading: CASN
Loading: CASP
Loading: CCYS
Loading: CCYX
Loading: CGLN
Loading: CGLU
Loading: CGLY
Loading: CHID
Loading: CHIE
Loading: CHIP
Loading: CHYP
Loading: CILE
Loading: CLEU
Loading: CLYS
Loading: CMET
Loading: CPHE
Loading: CPRO
Loading: CSER
Loading: CTHR
Loading: CTRP
Loading: CTYR
Loading: CVAL
Loading: NHE
Loading: NME
>> loadOff aminont12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminont12.lib
Loading: ACE
Loading: NALA
Loading: NARG
Loading: NASN
Loading: NASP
Loading: NCYS
Loading: NCYX
Loading: NGLN
Loading: NGLU
Loading: NGLY
Loading: NHID
Loading: NHIE
Loading: NHIP
Loading: NILE
Loading: NLEU
Loading: NLYS
Loading: NMET
Loading: NPHE
Loading: NPRO
Loading: NSER
Loading: NTHR
Loading: NTRP
Loading: NTYR
Loading: NVAL
>> loadOff nucleic12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/nucleic12.lib
Loading: A
Loading: A3
Loading: A5
Loading: AN
Loading: C
Loading: C3
Loading: C5
Loading: CN
Loading: DA
Loading: DA3
Loading: DA5
Loading: DAN
Loading: DC
Loading: DC3
Loading: DC5
Loading: DCN
Loading: DG
Loading: DG3
Loading: DG5
Loading: DGN
Loading: DT
Loading: DT3
Loading: DT5
Loading: DTN
Loading: G
Loading: G3
Loading: G5
Loading: GN
Loading: OHE
Loading: U
Loading: U3
Loading: U5
Loading: UN
>> #
>> #       Load water and ions
>> # 
>> loadOff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
>> loadOff solvents.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: MEOHBOX
Loading: NMABOX
Loading: OPC
Loading: OPCBOX
Loading: PL3
Loading: POL3BOX
Loading: QSPCFWBOX
Loading: SPC
Loading: SPCBOX
Loading: SPCFWBOX
Loading: SPF
Loading: SPG
Loading: T4E
Loading: TIP3PBOX
Loading: TIP3PFBOX
Loading: TIP4PBOX
Loading: TIP4PEWBOX
Loading: TIP5PBOX
Loading: TP3
Loading: TP4
Loading: TP5
Loading: TPF
>> HOH = TP3
>> WAT = TP3
>> 
>> #
>> #	Define the PDB name map for the amino acids and nucleic acids
>> #     (note: no NHYP!  use neutral form for now)
>> #
>> addPdbResMap {
>>   { 0 "HYP" "HYP"  } { 1 "HYP" "CHYP" }
>>   { 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
>>   { 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
>>   { 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
>>   { 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
>>   { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
>>   { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
>>   { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
>>   { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
>>   { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
>>   { 0 "HID" "NHID" } { 1 "HID" "CHID" }
>>   { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
>>   { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
>>   { 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
>>   { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
>>   { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
>>   { 0 "MET" "NMET" } { 1 "MET" "CMET" }
>>   { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
>>   { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
>>   { 0 "SER" "NSER" } { 1 "SER" "CSER" }
>>   { 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
>>   { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
>>   { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
>>   { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
>>   { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
>>   { 0 "G" "G5"  } { 1 "G" "G3"  } 
>>   { 0 "A" "A5"  } { 1 "A" "A3"  } 
>>   { 0 "C" "C5"  } { 1 "C" "C3"  } 
>>   { 0 "U" "U5"  } { 1 "U" "U3"  } 
>>   { 0 "DG" "DG5"  } { 1 "DG" "DG3"  }  
>>   { 0 "DA" "DA5"  } { 1 "DA" "DA3"  }  
>>   { 0 "DC" "DC5"  } { 1 "DC" "DC3"  }  
>>   { 0 "DT" "DT5"  } { 1 "DT" "DT3"  }  
>> #  some old Amber residue names for RNA:
>>   { 0  "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" }
>>   { 0  "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" }
>>   { 0  "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" }
>>   { 0  "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" }
>> #  some really old Amber residue names, assuming DNA:
>>   { 0 "GUA" "DG5"  } { 1 "GUA" "DG3"  } { "GUA" "DG" }
>>   { 0 "ADE" "DA5"  } { 1 "ADE" "DA3"  } { "ADE" "DA" }
>>   { 0 "CYT" "DC5"  } { 1 "CYT" "DC3"  } { "CYT" "DC" }
>>   { 0 "THY" "DT5"  } { 1 "THY" "DT3"  } { "THY" "DT" }
>> #  uncomment out the following if you have this old style RNA files:
>> # { 0 "GUA" "G5"  } { 1 "GUA" "G3"  } { "GUA" "G" }
>> # { 0 "ADE" "A5"  } { 1 "ADE" "A3"  } { "ADE" "A" }
>> # { 0 "CYT" "C5"  } { 1 "CYT" "C3"  } { "CYT" "C" }
>> # { 0 "URA" "R5"  } { 1 "URA" "R3"  } { "URA" "R" }
>> 
>> }
>> 
>> #  try to be good about reading in really old atom names as well:
>> addPdbAtomMap {
>>   { "O5*" "O5'" }
>>   { "C5*" "C5'" }
>>   { "C4*" "C4'" }
>>   { "O4*" "O4'" }
>>   { "C3*" "C3'" }
>>   { "O3*" "O3'" }
>>   { "C2*" "C2'" }
>>   { "O2*" "O2'" }
>>   { "C1*" "C1'" }
>>   { "C5M" "C7"  }
>>   { "H1*" "H1'" }
>>   { "H2*1" "H2'" }
>>   { "H2*2" "H2''" }
>>   { "HO*2" "HO2'" }
>>   { "H2'1" "H2'" }
>>   { "H2'2" "H2''" }
>>   { "H3*" "H3'" }
>>   { "H4*" "H4'" }
>>   { "H5*1" "H5'" }
>>   { "H5*2" "H5''" }
>>   { "H5'1" "H5'" }
>>   { "H5'2" "H5''" }
>>   { "HO'2" "HO2'" }
>>   { "H5T"  "HO5'" }
>>   { "H3T"  "HO3'" }
>>   { "O1'" "O4'" }
>>   { "OA"  "OP1" }
>>   { "OB"  "OP2" }
>>   { "O1P" "OP1" }
>>   { "O2P" "OP2" }
>> }
>> 
>> #
>> # assume that most often proteins use HIE
>> #
>> NHIS = NHIE
>> HIS = HIE
>> CHIS = CHIE
> 
> loadoff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
> loadamberparams frcmod.opc
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.opc
Reading force field modification type file (frcmod)
Reading title:
Parameters for OPC water (JPCL, 2014, 5 (21), pp 3863–3871) 
(UNKNOWN ATOM TYPE: EP)
> loadamberparams frcmod.ionsjc_tip4pew
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip4pew
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP4P/EW water from Joung & Cheatham JPCB (2008)
> 
> m = loadpdb init.pdb
Loading PDB file: ./init.pdb
Enter zPdbReadScan from call depth  0.
Exit  zPdbReadScan from call depth  0.
Matching PDB residue names to LEaP variables.
(Residue 0: A5, Terminal/beginning, was not found in name map.)
(Residue 1: C3, Terminal/last, was not found in name map.)
Joining A5 - C3
  total atoms in file: 63
> 
> 
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.131155 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<H4' 9>
Warning: Close contact of 1.307451 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<C4' 8>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> solvatebox m OPCBOX 9 iso
  Solute vdw bounding box:              12.265 11.150 10.292
  Total bounding box for atom centers:  30.265 30.265 30.265
      (box expansion for 'iso' is  11.1%)
  Solvent unit box:                     18.865 18.478 19.006
The number of boxes:  x= 2  y= 2  z= 2
Adding box at: x=0  y=0  z=0
Center of solvent box is: 9.432422, 9.239054, 9.503120
Adding box at: x=0  y=0  z=1
Center of solvent box is: 9.432422, 9.239054, -9.503120
Adding box at: x=0  y=1  z=0
Center of solvent box is: 9.432422, -9.239054, 9.503120
Adding box at: x=0  y=1  z=1
Center of solvent box is: 9.432422, -9.239054, -9.503120
Adding box at: x=1  y=0  z=0
Center of solvent box is: -9.432422, 9.239054, 9.503120
Adding box at: x=1  y=0  z=1
Center of solvent box is: -9.432422, 9.239054, -9.503120
Adding box at: x=1  y=1  z=0
Center of solvent box is: -9.432422, -9.239054, 9.503120
Adding box at: x=1  y=1  z=1
Center of solvent box is: -9.432422, -9.239054, -9.503120
  Volume: 37395.089 A^3 
  Total mass 14713.992 amu,  Density 0.653 g/cc
  Added 785 residues.
> quit
	Quit
log started: Sun Nov  1 20:53:02 2015

Log file: ./leap.log
>> #
>> # ----- leaprc for loading the ff12SB force field
>> # ----- NOTE: this is designed for PDB format 3!
>> #    Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA
>> #
>> #	load atom type hybridizations
>> #
>> addAtomTypes {
>> 	{ "H"   "H" "sp3" }
>> 	{ "HO"  "H" "sp3" }
>> 	{ "HS"  "H" "sp3" }
>> 	{ "H1"  "H" "sp3" }
>> 	{ "H2"  "H" "sp3" }
>> 	{ "H3"  "H" "sp3" }
>> 	{ "H4"  "H" "sp3" }
>> 	{ "H5"  "H" "sp3" }
>> 	{ "HW"  "H" "sp3" }
>> 	{ "HC"  "H" "sp3" }
>> 	{ "HA"  "H" "sp3" }
>> 	{ "HP"  "H" "sp3" }
>> 	{ "HZ"  "H" "sp3" }
>> 	{ "OH"  "O" "sp3" }
>> 	{ "OS"  "O" "sp3" }
>> 	{ "O"   "O" "sp2" }
>> 	{ "O2"  "O" "sp2" }
>> 	{ "OP"  "O" "sp2" }
>> 	{ "OW"  "O" "sp3" }
>> 	{ "CT"  "C" "sp3" }
>> 	{ "CX"  "C" "sp3" }
>> 	{ "C8"  "C" "sp3" }
>> 	{ "2C"  "C" "sp3" }
>> 	{ "3C"  "C" "sp3" }
>> 	{ "CH"  "C" "sp3" }
>> 	{ "CS"  "C" "sp2" }
>> 	{ "C"   "C" "sp2" }
>> 	{ "CO"   "C" "sp2" }
>> 	{ "C*"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CB"  "C" "sp2" }
>> 	{ "CC"  "C" "sp2" }
>> 	{ "CN"  "C" "sp2" }
>> 	{ "CM"  "C" "sp2" }
>> 	{ "CK"  "C" "sp2" }
>> 	{ "CQ"  "C" "sp2" }
>> 	{ "CD"  "C" "sp2" }
>> 	{ "C5"  "C" "sp2" }
>> 	{ "C4"  "C" "sp2" }
>> 	{ "CP"  "C" "sp2" }
>> 	{ "CI"  "C" "sp3" }
>> 	{ "CJ"  "C" "sp2" }
>> 	{ "CW"  "C" "sp2" }
>> 	{ "CV"  "C" "sp2" }
>> 	{ "CR"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CY"  "C" "sp2" }
>> 	{ "C0"  "Ca" "sp3" }
>> 	{ "MG"  "Mg" "sp3" }
>> 	{ "N"   "N" "sp2" }
>> 	{ "NA"  "N" "sp2" }
>> 	{ "N2"  "N" "sp2" }
>> 	{ "N*"  "N" "sp2" }
>> 	{ "NP"  "N" "sp2" }
>> 	{ "NQ"  "N" "sp2" }
>> 	{ "NB"  "N" "sp2" }
>> 	{ "NC"  "N" "sp2" }
>> 	{ "NT"  "N" "sp3" }
>> 	{ "NY"  "N" "sp2" }
>> 	{ "N3"  "N" "sp3" }
>> 	{ "S"   "S" "sp3" }
>> 	{ "SH"  "S" "sp3" }
>> 	{ "P"   "P" "sp3" }
>> 	{ "LP"  ""  "sp3" }
>> 	{ "EP"  ""  "sp3" }
>> 	{ "F"   "F" "sp3" }
>> 	{ "Cl"  "Cl" "sp3" }
>> 	{ "Br"  "Br" "sp3" }
>> 	{ "I"   "I"  "sp3" }
>> 	{ "F-"   "F" "sp3" }
>> 	{ "Cl-"  "Cl" "sp3" }
>> 	{ "Br-"  "Br" "sp3" }
>> 	{ "I-"   "I"  "sp3" }
>> 	{ "Li+"  "Li"  "sp3" }
>> 	{ "Na+"  "Na"  "sp3" }
>> 	{ "K+"  "K"  "sp3" }
>> 	{ "Rb+"  "Rb"  "sp3" }
>> 	{ "Cs+"  "Cs"  "sp3" }
>> 	{ "Mg+"  "Mg"  "sp3" }
>> # glycam
>> 	{ "OG"  "O" "sp3" }
>> 	{ "OL"  "O" "sp3" }
>> 	{ "AC"  "C" "sp3" }
>> 	{ "EC"  "C" "sp3" }
>> }
>> #
>> #	Load the main parameter set.
>> #
>> parm10 = loadamberparams parm10.dat
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
(UNKNOWN ATOM TYPE: Zn)
(UNKNOWN ATOM TYPE: EP)
>> frcmod12SB = loadamberparams frcmod.ff12SB
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff12SB
Reading force field modification type file (frcmod)
Reading title:
ff12SB protein backbone and sidechain parameters
>> #
>> #	Load main chain and terminating amino acid libraries, nucleic acids
>> #
>> loadOff amino12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/amino12.lib
Loading: ALA
Loading: ARG
Loading: ASH
Loading: ASN
Loading: ASP
Loading: CYM
Loading: CYS
Loading: CYX
Loading: GLH
Loading: GLN
Loading: GLU
Loading: GLY
Loading: HID
Loading: HIE
Loading: HIP
Loading: HYP
Loading: ILE
Loading: LEU
Loading: LYN
Loading: LYS
Loading: MET
Loading: PHE
Loading: PRO
Loading: SER
Loading: THR
Loading: TRP
Loading: TYR
Loading: VAL
>> loadOff aminoct12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminoct12.lib
Loading: CALA
Loading: CARG
Loading: CASN
Loading: CASP
Loading: CCYS
Loading: CCYX
Loading: CGLN
Loading: CGLU
Loading: CGLY
Loading: CHID
Loading: CHIE
Loading: CHIP
Loading: CHYP
Loading: CILE
Loading: CLEU
Loading: CLYS
Loading: CMET
Loading: CPHE
Loading: CPRO
Loading: CSER
Loading: CTHR
Loading: CTRP
Loading: CTYR
Loading: CVAL
Loading: NHE
Loading: NME
>> loadOff aminont12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminont12.lib
Loading: ACE
Loading: NALA
Loading: NARG
Loading: NASN
Loading: NASP
Loading: NCYS
Loading: NCYX
Loading: NGLN
Loading: NGLU
Loading: NGLY
Loading: NHID
Loading: NHIE
Loading: NHIP
Loading: NILE
Loading: NLEU
Loading: NLYS
Loading: NMET
Loading: NPHE
Loading: NPRO
Loading: NSER
Loading: NTHR
Loading: NTRP
Loading: NTYR
Loading: NVAL
>> loadOff nucleic12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/nucleic12.lib
Loading: A
Loading: A3
Loading: A5
Loading: AN
Loading: C
Loading: C3
Loading: C5
Loading: CN
Loading: DA
Loading: DA3
Loading: DA5
Loading: DAN
Loading: DC
Loading: DC3
Loading: DC5
Loading: DCN
Loading: DG
Loading: DG3
Loading: DG5
Loading: DGN
Loading: DT
Loading: DT3
Loading: DT5
Loading: DTN
Loading: G
Loading: G3
Loading: G5
Loading: GN
Loading: OHE
Loading: U
Loading: U3
Loading: U5
Loading: UN
>> #
>> #       Load water and ions
>> # 
>> loadOff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
>> loadOff solvents.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: MEOHBOX
Loading: NMABOX
Loading: OPC
Loading: OPCBOX
Loading: PL3
Loading: POL3BOX
Loading: QSPCFWBOX
Loading: SPC
Loading: SPCBOX
Loading: SPCFWBOX
Loading: SPF
Loading: SPG
Loading: T4E
Loading: TIP3PBOX
Loading: TIP3PFBOX
Loading: TIP4PBOX
Loading: TIP4PEWBOX
Loading: TIP5PBOX
Loading: TP3
Loading: TP4
Loading: TP5
Loading: TPF
>> HOH = TP3
>> WAT = TP3
>> 
>> #
>> #	Define the PDB name map for the amino acids and nucleic acids
>> #     (note: no NHYP!  use neutral form for now)
>> #
>> addPdbResMap {
>>   { 0 "HYP" "HYP"  } { 1 "HYP" "CHYP" }
>>   { 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
>>   { 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
>>   { 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
>>   { 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
>>   { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
>>   { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
>>   { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
>>   { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
>>   { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
>>   { 0 "HID" "NHID" } { 1 "HID" "CHID" }
>>   { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
>>   { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
>>   { 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
>>   { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
>>   { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
>>   { 0 "MET" "NMET" } { 1 "MET" "CMET" }
>>   { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
>>   { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
>>   { 0 "SER" "NSER" } { 1 "SER" "CSER" }
>>   { 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
>>   { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
>>   { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
>>   { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
>>   { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
>>   { 0 "G" "G5"  } { 1 "G" "G3"  } 
>>   { 0 "A" "A5"  } { 1 "A" "A3"  } 
>>   { 0 "C" "C5"  } { 1 "C" "C3"  } 
>>   { 0 "U" "U5"  } { 1 "U" "U3"  } 
>>   { 0 "DG" "DG5"  } { 1 "DG" "DG3"  }  
>>   { 0 "DA" "DA5"  } { 1 "DA" "DA3"  }  
>>   { 0 "DC" "DC5"  } { 1 "DC" "DC3"  }  
>>   { 0 "DT" "DT5"  } { 1 "DT" "DT3"  }  
>> #  some old Amber residue names for RNA:
>>   { 0  "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" }
>>   { 0  "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" }
>>   { 0  "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" }
>>   { 0  "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" }
>> #  some really old Amber residue names, assuming DNA:
>>   { 0 "GUA" "DG5"  } { 1 "GUA" "DG3"  } { "GUA" "DG" }
>>   { 0 "ADE" "DA5"  } { 1 "ADE" "DA3"  } { "ADE" "DA" }
>>   { 0 "CYT" "DC5"  } { 1 "CYT" "DC3"  } { "CYT" "DC" }
>>   { 0 "THY" "DT5"  } { 1 "THY" "DT3"  } { "THY" "DT" }
>> #  uncomment out the following if you have this old style RNA files:
>> # { 0 "GUA" "G5"  } { 1 "GUA" "G3"  } { "GUA" "G" }
>> # { 0 "ADE" "A5"  } { 1 "ADE" "A3"  } { "ADE" "A" }
>> # { 0 "CYT" "C5"  } { 1 "CYT" "C3"  } { "CYT" "C" }
>> # { 0 "URA" "R5"  } { 1 "URA" "R3"  } { "URA" "R" }
>> 
>> }
>> 
>> #  try to be good about reading in really old atom names as well:
>> addPdbAtomMap {
>>   { "O5*" "O5'" }
>>   { "C5*" "C5'" }
>>   { "C4*" "C4'" }
>>   { "O4*" "O4'" }
>>   { "C3*" "C3'" }
>>   { "O3*" "O3'" }
>>   { "C2*" "C2'" }
>>   { "O2*" "O2'" }
>>   { "C1*" "C1'" }
>>   { "C5M" "C7"  }
>>   { "H1*" "H1'" }
>>   { "H2*1" "H2'" }
>>   { "H2*2" "H2''" }
>>   { "HO*2" "HO2'" }
>>   { "H2'1" "H2'" }
>>   { "H2'2" "H2''" }
>>   { "H3*" "H3'" }
>>   { "H4*" "H4'" }
>>   { "H5*1" "H5'" }
>>   { "H5*2" "H5''" }
>>   { "H5'1" "H5'" }
>>   { "H5'2" "H5''" }
>>   { "HO'2" "HO2'" }
>>   { "H5T"  "HO5'" }
>>   { "H3T"  "HO3'" }
>>   { "O1'" "O4'" }
>>   { "OA"  "OP1" }
>>   { "OB"  "OP2" }
>>   { "O1P" "OP1" }
>>   { "O2P" "OP2" }
>> }
>> 
>> #
>> # assume that most often proteins use HIE
>> #
>> NHIS = NHIE
>> HIS = HIE
>> CHIS = CHIE
> 
> loadoff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
> loadamberparams frcmod.opc
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.opc
Reading force field modification type file (frcmod)
Reading title:
Parameters for OPC water (JPCL, 2014, 5 (21), pp 3863–3871) 
(UNKNOWN ATOM TYPE: EP)
> loadamberparams frcmod.ionsjc_tip4pew
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip4pew
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP4P/EW water from Joung & Cheatham JPCB (2008)
> 
> m = loadpdb init.pdb
Loading PDB file: ./init.pdb
Enter zPdbReadScan from call depth  0.
Exit  zPdbReadScan from call depth  0.
Matching PDB residue names to LEaP variables.
(Residue 0: A5, Terminal/beginning, was not found in name map.)
(Residue 1: C3, Terminal/last, was not found in name map.)
Joining A5 - C3
  total atoms in file: 63
> 
> 
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.131155 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<H4' 9>
Warning: Close contact of 1.307451 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<C4' 8>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> solvatebox m OPCBOX 10 iso
  Solute vdw bounding box:              12.265 11.150 10.292
  Total bounding box for atom centers:  32.265 32.265 32.265
      (box expansion for 'iso' is  10.3%)
  Solvent unit box:                     18.865 18.478 19.006
The number of boxes:  x= 2  y= 2  z= 2
Adding box at: x=0  y=0  z=0
Center of solvent box is: 9.432422, 9.239054, 9.503120
Adding box at: x=0  y=0  z=1
Center of solvent box is: 9.432422, 9.239054, -9.503120
Adding box at: x=0  y=1  z=0
Center of solvent box is: 9.432422, -9.239054, 9.503120
Adding box at: x=0  y=1  z=1
Center of solvent box is: 9.432422, -9.239054, -9.503120
Adding box at: x=1  y=0  z=0
Center of solvent box is: -9.432422, 9.239054, 9.503120
Adding box at: x=1  y=0  z=1
Center of solvent box is: -9.432422, 9.239054, -9.503120
Adding box at: x=1  y=1  z=0
Center of solvent box is: -9.432422, -9.239054, 9.503120
Adding box at: x=1  y=1  z=1
Center of solvent box is: -9.432422, -9.239054, -9.503120
  Volume: 44008.365 A^3 
  Total mass 17758.696 amu,  Density 0.670 g/cc
  Added 954 residues.
> quit
	Quit
log started: Sun Nov  1 20:53:02 2015

Log file: ./leap.log
>> #
>> # ----- leaprc for loading the ff12SB force field
>> # ----- NOTE: this is designed for PDB format 3!
>> #    Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA
>> #
>> #	load atom type hybridizations
>> #
>> addAtomTypes {
>> 	{ "H"   "H" "sp3" }
>> 	{ "HO"  "H" "sp3" }
>> 	{ "HS"  "H" "sp3" }
>> 	{ "H1"  "H" "sp3" }
>> 	{ "H2"  "H" "sp3" }
>> 	{ "H3"  "H" "sp3" }
>> 	{ "H4"  "H" "sp3" }
>> 	{ "H5"  "H" "sp3" }
>> 	{ "HW"  "H" "sp3" }
>> 	{ "HC"  "H" "sp3" }
>> 	{ "HA"  "H" "sp3" }
>> 	{ "HP"  "H" "sp3" }
>> 	{ "HZ"  "H" "sp3" }
>> 	{ "OH"  "O" "sp3" }
>> 	{ "OS"  "O" "sp3" }
>> 	{ "O"   "O" "sp2" }
>> 	{ "O2"  "O" "sp2" }
>> 	{ "OP"  "O" "sp2" }
>> 	{ "OW"  "O" "sp3" }
>> 	{ "CT"  "C" "sp3" }
>> 	{ "CX"  "C" "sp3" }
>> 	{ "C8"  "C" "sp3" }
>> 	{ "2C"  "C" "sp3" }
>> 	{ "3C"  "C" "sp3" }
>> 	{ "CH"  "C" "sp3" }
>> 	{ "CS"  "C" "sp2" }
>> 	{ "C"   "C" "sp2" }
>> 	{ "CO"   "C" "sp2" }
>> 	{ "C*"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CB"  "C" "sp2" }
>> 	{ "CC"  "C" "sp2" }
>> 	{ "CN"  "C" "sp2" }
>> 	{ "CM"  "C" "sp2" }
>> 	{ "CK"  "C" "sp2" }
>> 	{ "CQ"  "C" "sp2" }
>> 	{ "CD"  "C" "sp2" }
>> 	{ "C5"  "C" "sp2" }
>> 	{ "C4"  "C" "sp2" }
>> 	{ "CP"  "C" "sp2" }
>> 	{ "CI"  "C" "sp3" }
>> 	{ "CJ"  "C" "sp2" }
>> 	{ "CW"  "C" "sp2" }
>> 	{ "CV"  "C" "sp2" }
>> 	{ "CR"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CY"  "C" "sp2" }
>> 	{ "C0"  "Ca" "sp3" }
>> 	{ "MG"  "Mg" "sp3" }
>> 	{ "N"   "N" "sp2" }
>> 	{ "NA"  "N" "sp2" }
>> 	{ "N2"  "N" "sp2" }
>> 	{ "N*"  "N" "sp2" }
>> 	{ "NP"  "N" "sp2" }
>> 	{ "NQ"  "N" "sp2" }
>> 	{ "NB"  "N" "sp2" }
>> 	{ "NC"  "N" "sp2" }
>> 	{ "NT"  "N" "sp3" }
>> 	{ "NY"  "N" "sp2" }
>> 	{ "N3"  "N" "sp3" }
>> 	{ "S"   "S" "sp3" }
>> 	{ "SH"  "S" "sp3" }
>> 	{ "P"   "P" "sp3" }
>> 	{ "LP"  ""  "sp3" }
>> 	{ "EP"  ""  "sp3" }
>> 	{ "F"   "F" "sp3" }
>> 	{ "Cl"  "Cl" "sp3" }
>> 	{ "Br"  "Br" "sp3" }
>> 	{ "I"   "I"  "sp3" }
>> 	{ "F-"   "F" "sp3" }
>> 	{ "Cl-"  "Cl" "sp3" }
>> 	{ "Br-"  "Br" "sp3" }
>> 	{ "I-"   "I"  "sp3" }
>> 	{ "Li+"  "Li"  "sp3" }
>> 	{ "Na+"  "Na"  "sp3" }
>> 	{ "K+"  "K"  "sp3" }
>> 	{ "Rb+"  "Rb"  "sp3" }
>> 	{ "Cs+"  "Cs"  "sp3" }
>> 	{ "Mg+"  "Mg"  "sp3" }
>> # glycam
>> 	{ "OG"  "O" "sp3" }
>> 	{ "OL"  "O" "sp3" }
>> 	{ "AC"  "C" "sp3" }
>> 	{ "EC"  "C" "sp3" }
>> }
>> #
>> #	Load the main parameter set.
>> #
>> parm10 = loadamberparams parm10.dat
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
(UNKNOWN ATOM TYPE: Zn)
(UNKNOWN ATOM TYPE: EP)
>> frcmod12SB = loadamberparams frcmod.ff12SB
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff12SB
Reading force field modification type file (frcmod)
Reading title:
ff12SB protein backbone and sidechain parameters
>> #
>> #	Load main chain and terminating amino acid libraries, nucleic acids
>> #
>> loadOff amino12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/amino12.lib
Loading: ALA
Loading: ARG
Loading: ASH
Loading: ASN
Loading: ASP
Loading: CYM
Loading: CYS
Loading: CYX
Loading: GLH
Loading: GLN
Loading: GLU
Loading: GLY
Loading: HID
Loading: HIE
Loading: HIP
Loading: HYP
Loading: ILE
Loading: LEU
Loading: LYN
Loading: LYS
Loading: MET
Loading: PHE
Loading: PRO
Loading: SER
Loading: THR
Loading: TRP
Loading: TYR
Loading: VAL
>> loadOff aminoct12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminoct12.lib
Loading: CALA
Loading: CARG
Loading: CASN
Loading: CASP
Loading: CCYS
Loading: CCYX
Loading: CGLN
Loading: CGLU
Loading: CGLY
Loading: CHID
Loading: CHIE
Loading: CHIP
Loading: CHYP
Loading: CILE
Loading: CLEU
Loading: CLYS
Loading: CMET
Loading: CPHE
Loading: CPRO
Loading: CSER
Loading: CTHR
Loading: CTRP
Loading: CTYR
Loading: CVAL
Loading: NHE
Loading: NME
>> loadOff aminont12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminont12.lib
Loading: ACE
Loading: NALA
Loading: NARG
Loading: NASN
Loading: NASP
Loading: NCYS
Loading: NCYX
Loading: NGLN
Loading: NGLU
Loading: NGLY
Loading: NHID
Loading: NHIE
Loading: NHIP
Loading: NILE
Loading: NLEU
Loading: NLYS
Loading: NMET
Loading: NPHE
Loading: NPRO
Loading: NSER
Loading: NTHR
Loading: NTRP
Loading: NTYR
Loading: NVAL
>> loadOff nucleic12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/nucleic12.lib
Loading: A
Loading: A3
Loading: A5
Loading: AN
Loading: C
Loading: C3
Loading: C5
Loading: CN
Loading: DA
Loading: DA3
Loading: DA5
Loading: DAN
Loading: DC
Loading: DC3
Loading: DC5
Loading: DCN
Loading: DG
Loading: DG3
Loading: DG5
Loading: DGN
Loading: DT
Loading: DT3
Loading: DT5
Loading: DTN
Loading: G
Loading: G3
Loading: G5
Loading: GN
Loading: OHE
Loading: U
Loading: U3
Loading: U5
Loading: UN
>> #
>> #       Load water and ions
>> # 
>> loadOff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
>> loadOff solvents.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: MEOHBOX
Loading: NMABOX
Loading: OPC
Loading: OPCBOX
Loading: PL3
Loading: POL3BOX
Loading: QSPCFWBOX
Loading: SPC
Loading: SPCBOX
Loading: SPCFWBOX
Loading: SPF
Loading: SPG
Loading: T4E
Loading: TIP3PBOX
Loading: TIP3PFBOX
Loading: TIP4PBOX
Loading: TIP4PEWBOX
Loading: TIP5PBOX
Loading: TP3
Loading: TP4
Loading: TP5
Loading: TPF
>> HOH = TP3
>> WAT = TP3
>> 
>> #
>> #	Define the PDB name map for the amino acids and nucleic acids
>> #     (note: no NHYP!  use neutral form for now)
>> #
>> addPdbResMap {
>>   { 0 "HYP" "HYP"  } { 1 "HYP" "CHYP" }
>>   { 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
>>   { 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
>>   { 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
>>   { 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
>>   { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
>>   { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
>>   { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
>>   { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
>>   { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
>>   { 0 "HID" "NHID" } { 1 "HID" "CHID" }
>>   { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
>>   { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
>>   { 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
>>   { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
>>   { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
>>   { 0 "MET" "NMET" } { 1 "MET" "CMET" }
>>   { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
>>   { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
>>   { 0 "SER" "NSER" } { 1 "SER" "CSER" }
>>   { 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
>>   { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
>>   { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
>>   { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
>>   { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
>>   { 0 "G" "G5"  } { 1 "G" "G3"  } 
>>   { 0 "A" "A5"  } { 1 "A" "A3"  } 
>>   { 0 "C" "C5"  } { 1 "C" "C3"  } 
>>   { 0 "U" "U5"  } { 1 "U" "U3"  } 
>>   { 0 "DG" "DG5"  } { 1 "DG" "DG3"  }  
>>   { 0 "DA" "DA5"  } { 1 "DA" "DA3"  }  
>>   { 0 "DC" "DC5"  } { 1 "DC" "DC3"  }  
>>   { 0 "DT" "DT5"  } { 1 "DT" "DT3"  }  
>> #  some old Amber residue names for RNA:
>>   { 0  "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" }
>>   { 0  "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" }
>>   { 0  "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" }
>>   { 0  "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" }
>> #  some really old Amber residue names, assuming DNA:
>>   { 0 "GUA" "DG5"  } { 1 "GUA" "DG3"  } { "GUA" "DG" }
>>   { 0 "ADE" "DA5"  } { 1 "ADE" "DA3"  } { "ADE" "DA" }
>>   { 0 "CYT" "DC5"  } { 1 "CYT" "DC3"  } { "CYT" "DC" }
>>   { 0 "THY" "DT5"  } { 1 "THY" "DT3"  } { "THY" "DT" }
>> #  uncomment out the following if you have this old style RNA files:
>> # { 0 "GUA" "G5"  } { 1 "GUA" "G3"  } { "GUA" "G" }
>> # { 0 "ADE" "A5"  } { 1 "ADE" "A3"  } { "ADE" "A" }
>> # { 0 "CYT" "C5"  } { 1 "CYT" "C3"  } { "CYT" "C" }
>> # { 0 "URA" "R5"  } { 1 "URA" "R3"  } { "URA" "R" }
>> 
>> }
>> 
>> #  try to be good about reading in really old atom names as well:
>> addPdbAtomMap {
>>   { "O5*" "O5'" }
>>   { "C5*" "C5'" }
>>   { "C4*" "C4'" }
>>   { "O4*" "O4'" }
>>   { "C3*" "C3'" }
>>   { "O3*" "O3'" }
>>   { "C2*" "C2'" }
>>   { "O2*" "O2'" }
>>   { "C1*" "C1'" }
>>   { "C5M" "C7"  }
>>   { "H1*" "H1'" }
>>   { "H2*1" "H2'" }
>>   { "H2*2" "H2''" }
>>   { "HO*2" "HO2'" }
>>   { "H2'1" "H2'" }
>>   { "H2'2" "H2''" }
>>   { "H3*" "H3'" }
>>   { "H4*" "H4'" }
>>   { "H5*1" "H5'" }
>>   { "H5*2" "H5''" }
>>   { "H5'1" "H5'" }
>>   { "H5'2" "H5''" }
>>   { "HO'2" "HO2'" }
>>   { "H5T"  "HO5'" }
>>   { "H3T"  "HO3'" }
>>   { "O1'" "O4'" }
>>   { "OA"  "OP1" }
>>   { "OB"  "OP2" }
>>   { "O1P" "OP1" }
>>   { "O2P" "OP2" }
>> }
>> 
>> #
>> # assume that most often proteins use HIE
>> #
>> NHIS = NHIE
>> HIS = HIE
>> CHIS = CHIE
> 
> loadoff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
> loadamberparams frcmod.opc
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.opc
Reading force field modification type file (frcmod)
Reading title:
Parameters for OPC water (JPCL, 2014, 5 (21), pp 3863–3871) 
(UNKNOWN ATOM TYPE: EP)
> loadamberparams frcmod.ionsjc_tip4pew
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip4pew
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP4P/EW water from Joung & Cheatham JPCB (2008)
> 
> m = loadpdb init.pdb
Loading PDB file: ./init.pdb
Enter zPdbReadScan from call depth  0.
Exit  zPdbReadScan from call depth  0.
Matching PDB residue names to LEaP variables.
(Residue 0: A5, Terminal/beginning, was not found in name map.)
(Residue 1: C3, Terminal/last, was not found in name map.)
Joining A5 - C3
  total atoms in file: 63
> 
> 
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.131155 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<H4' 9>
Warning: Close contact of 1.307451 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<C4' 8>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> solvatebox m OPCBOX 11 iso
  Solute vdw bounding box:              12.265 11.150 10.292
  Total bounding box for atom centers:  34.265 34.265 34.265
      (box expansion for 'iso' is   9.7%)
  Solvent unit box:                     18.865 18.478 19.006
The number of boxes:  x= 2  y= 2  z= 2
Adding box at: x=0  y=0  z=0
Center of solvent box is: 9.432422, 9.239054, 9.503120
Adding box at: x=0  y=0  z=1
Center of solvent box is: 9.432422, 9.239054, -9.503120
Adding box at: x=0  y=1  z=0
Center of solvent box is: 9.432422, -9.239054, 9.503120
Adding box at: x=0  y=1  z=1
Center of solvent box is: 9.432422, -9.239054, -9.503120
Adding box at: x=1  y=0  z=0
Center of solvent box is: -9.432422, 9.239054, 9.503120
Adding box at: x=1  y=0  z=1
Center of solvent box is: -9.432422, 9.239054, -9.503120
Adding box at: x=1  y=1  z=0
Center of solvent box is: -9.432422, -9.239054, 9.503120
Adding box at: x=1  y=1  z=1
Center of solvent box is: -9.432422, -9.239054, -9.503120
  Volume: 52632.886 A^3 
  Total mass 22118.568 amu,  Density 0.698 g/cc
  Added 1196 residues.
> quit
	Quit
log started: Sun Nov  1 20:53:02 2015

Log file: ./leap.log
>> #
>> # ----- leaprc for loading the ff12SB force field
>> # ----- NOTE: this is designed for PDB format 3!
>> #    Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA
>> #
>> #	load atom type hybridizations
>> #
>> addAtomTypes {
>> 	{ "H"   "H" "sp3" }
>> 	{ "HO"  "H" "sp3" }
>> 	{ "HS"  "H" "sp3" }
>> 	{ "H1"  "H" "sp3" }
>> 	{ "H2"  "H" "sp3" }
>> 	{ "H3"  "H" "sp3" }
>> 	{ "H4"  "H" "sp3" }
>> 	{ "H5"  "H" "sp3" }
>> 	{ "HW"  "H" "sp3" }
>> 	{ "HC"  "H" "sp3" }
>> 	{ "HA"  "H" "sp3" }
>> 	{ "HP"  "H" "sp3" }
>> 	{ "HZ"  "H" "sp3" }
>> 	{ "OH"  "O" "sp3" }
>> 	{ "OS"  "O" "sp3" }
>> 	{ "O"   "O" "sp2" }
>> 	{ "O2"  "O" "sp2" }
>> 	{ "OP"  "O" "sp2" }
>> 	{ "OW"  "O" "sp3" }
>> 	{ "CT"  "C" "sp3" }
>> 	{ "CX"  "C" "sp3" }
>> 	{ "C8"  "C" "sp3" }
>> 	{ "2C"  "C" "sp3" }
>> 	{ "3C"  "C" "sp3" }
>> 	{ "CH"  "C" "sp3" }
>> 	{ "CS"  "C" "sp2" }
>> 	{ "C"   "C" "sp2" }
>> 	{ "CO"   "C" "sp2" }
>> 	{ "C*"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CB"  "C" "sp2" }
>> 	{ "CC"  "C" "sp2" }
>> 	{ "CN"  "C" "sp2" }
>> 	{ "CM"  "C" "sp2" }
>> 	{ "CK"  "C" "sp2" }
>> 	{ "CQ"  "C" "sp2" }
>> 	{ "CD"  "C" "sp2" }
>> 	{ "C5"  "C" "sp2" }
>> 	{ "C4"  "C" "sp2" }
>> 	{ "CP"  "C" "sp2" }
>> 	{ "CI"  "C" "sp3" }
>> 	{ "CJ"  "C" "sp2" }
>> 	{ "CW"  "C" "sp2" }
>> 	{ "CV"  "C" "sp2" }
>> 	{ "CR"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CY"  "C" "sp2" }
>> 	{ "C0"  "Ca" "sp3" }
>> 	{ "MG"  "Mg" "sp3" }
>> 	{ "N"   "N" "sp2" }
>> 	{ "NA"  "N" "sp2" }
>> 	{ "N2"  "N" "sp2" }
>> 	{ "N*"  "N" "sp2" }
>> 	{ "NP"  "N" "sp2" }
>> 	{ "NQ"  "N" "sp2" }
>> 	{ "NB"  "N" "sp2" }
>> 	{ "NC"  "N" "sp2" }
>> 	{ "NT"  "N" "sp3" }
>> 	{ "NY"  "N" "sp2" }
>> 	{ "N3"  "N" "sp3" }
>> 	{ "S"   "S" "sp3" }
>> 	{ "SH"  "S" "sp3" }
>> 	{ "P"   "P" "sp3" }
>> 	{ "LP"  ""  "sp3" }
>> 	{ "EP"  ""  "sp3" }
>> 	{ "F"   "F" "sp3" }
>> 	{ "Cl"  "Cl" "sp3" }
>> 	{ "Br"  "Br" "sp3" }
>> 	{ "I"   "I"  "sp3" }
>> 	{ "F-"   "F" "sp3" }
>> 	{ "Cl-"  "Cl" "sp3" }
>> 	{ "Br-"  "Br" "sp3" }
>> 	{ "I-"   "I"  "sp3" }
>> 	{ "Li+"  "Li"  "sp3" }
>> 	{ "Na+"  "Na"  "sp3" }
>> 	{ "K+"  "K"  "sp3" }
>> 	{ "Rb+"  "Rb"  "sp3" }
>> 	{ "Cs+"  "Cs"  "sp3" }
>> 	{ "Mg+"  "Mg"  "sp3" }
>> # glycam
>> 	{ "OG"  "O" "sp3" }
>> 	{ "OL"  "O" "sp3" }
>> 	{ "AC"  "C" "sp3" }
>> 	{ "EC"  "C" "sp3" }
>> }
>> #
>> #	Load the main parameter set.
>> #
>> parm10 = loadamberparams parm10.dat
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
(UNKNOWN ATOM TYPE: Zn)
(UNKNOWN ATOM TYPE: EP)
>> frcmod12SB = loadamberparams frcmod.ff12SB
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff12SB
Reading force field modification type file (frcmod)
Reading title:
ff12SB protein backbone and sidechain parameters
>> #
>> #	Load main chain and terminating amino acid libraries, nucleic acids
>> #
>> loadOff amino12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/amino12.lib
Loading: ALA
Loading: ARG
Loading: ASH
Loading: ASN
Loading: ASP
Loading: CYM
Loading: CYS
Loading: CYX
Loading: GLH
Loading: GLN
Loading: GLU
Loading: GLY
Loading: HID
Loading: HIE
Loading: HIP
Loading: HYP
Loading: ILE
Loading: LEU
Loading: LYN
Loading: LYS
Loading: MET
Loading: PHE
Loading: PRO
Loading: SER
Loading: THR
Loading: TRP
Loading: TYR
Loading: VAL
>> loadOff aminoct12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminoct12.lib
Loading: CALA
Loading: CARG
Loading: CASN
Loading: CASP
Loading: CCYS
Loading: CCYX
Loading: CGLN
Loading: CGLU
Loading: CGLY
Loading: CHID
Loading: CHIE
Loading: CHIP
Loading: CHYP
Loading: CILE
Loading: CLEU
Loading: CLYS
Loading: CMET
Loading: CPHE
Loading: CPRO
Loading: CSER
Loading: CTHR
Loading: CTRP
Loading: CTYR
Loading: CVAL
Loading: NHE
Loading: NME
>> loadOff aminont12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminont12.lib
Loading: ACE
Loading: NALA
Loading: NARG
Loading: NASN
Loading: NASP
Loading: NCYS
Loading: NCYX
Loading: NGLN
Loading: NGLU
Loading: NGLY
Loading: NHID
Loading: NHIE
Loading: NHIP
Loading: NILE
Loading: NLEU
Loading: NLYS
Loading: NMET
Loading: NPHE
Loading: NPRO
Loading: NSER
Loading: NTHR
Loading: NTRP
Loading: NTYR
Loading: NVAL
>> loadOff nucleic12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/nucleic12.lib
Loading: A
Loading: A3
Loading: A5
Loading: AN
Loading: C
Loading: C3
Loading: C5
Loading: CN
Loading: DA
Loading: DA3
Loading: DA5
Loading: DAN
Loading: DC
Loading: DC3
Loading: DC5
Loading: DCN
Loading: DG
Loading: DG3
Loading: DG5
Loading: DGN
Loading: DT
Loading: DT3
Loading: DT5
Loading: DTN
Loading: G
Loading: G3
Loading: G5
Loading: GN
Loading: OHE
Loading: U
Loading: U3
Loading: U5
Loading: UN
>> #
>> #       Load water and ions
>> # 
>> loadOff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
>> loadOff solvents.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: MEOHBOX
Loading: NMABOX
Loading: OPC
Loading: OPCBOX
Loading: PL3
Loading: POL3BOX
Loading: QSPCFWBOX
Loading: SPC
Loading: SPCBOX
Loading: SPCFWBOX
Loading: SPF
Loading: SPG
Loading: T4E
Loading: TIP3PBOX
Loading: TIP3PFBOX
Loading: TIP4PBOX
Loading: TIP4PEWBOX
Loading: TIP5PBOX
Loading: TP3
Loading: TP4
Loading: TP5
Loading: TPF
>> HOH = TP3
>> WAT = TP3
>> 
>> #
>> #	Define the PDB name map for the amino acids and nucleic acids
>> #     (note: no NHYP!  use neutral form for now)
>> #
>> addPdbResMap {
>>   { 0 "HYP" "HYP"  } { 1 "HYP" "CHYP" }
>>   { 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
>>   { 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
>>   { 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
>>   { 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
>>   { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
>>   { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
>>   { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
>>   { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
>>   { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
>>   { 0 "HID" "NHID" } { 1 "HID" "CHID" }
>>   { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
>>   { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
>>   { 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
>>   { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
>>   { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
>>   { 0 "MET" "NMET" } { 1 "MET" "CMET" }
>>   { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
>>   { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
>>   { 0 "SER" "NSER" } { 1 "SER" "CSER" }
>>   { 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
>>   { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
>>   { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
>>   { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
>>   { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
>>   { 0 "G" "G5"  } { 1 "G" "G3"  } 
>>   { 0 "A" "A5"  } { 1 "A" "A3"  } 
>>   { 0 "C" "C5"  } { 1 "C" "C3"  } 
>>   { 0 "U" "U5"  } { 1 "U" "U3"  } 
>>   { 0 "DG" "DG5"  } { 1 "DG" "DG3"  }  
>>   { 0 "DA" "DA5"  } { 1 "DA" "DA3"  }  
>>   { 0 "DC" "DC5"  } { 1 "DC" "DC3"  }  
>>   { 0 "DT" "DT5"  } { 1 "DT" "DT3"  }  
>> #  some old Amber residue names for RNA:
>>   { 0  "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" }
>>   { 0  "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" }
>>   { 0  "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" }
>>   { 0  "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" }
>> #  some really old Amber residue names, assuming DNA:
>>   { 0 "GUA" "DG5"  } { 1 "GUA" "DG3"  } { "GUA" "DG" }
>>   { 0 "ADE" "DA5"  } { 1 "ADE" "DA3"  } { "ADE" "DA" }
>>   { 0 "CYT" "DC5"  } { 1 "CYT" "DC3"  } { "CYT" "DC" }
>>   { 0 "THY" "DT5"  } { 1 "THY" "DT3"  } { "THY" "DT" }
>> #  uncomment out the following if you have this old style RNA files:
>> # { 0 "GUA" "G5"  } { 1 "GUA" "G3"  } { "GUA" "G" }
>> # { 0 "ADE" "A5"  } { 1 "ADE" "A3"  } { "ADE" "A" }
>> # { 0 "CYT" "C5"  } { 1 "CYT" "C3"  } { "CYT" "C" }
>> # { 0 "URA" "R5"  } { 1 "URA" "R3"  } { "URA" "R" }
>> 
>> }
>> 
>> #  try to be good about reading in really old atom names as well:
>> addPdbAtomMap {
>>   { "O5*" "O5'" }
>>   { "C5*" "C5'" }
>>   { "C4*" "C4'" }
>>   { "O4*" "O4'" }
>>   { "C3*" "C3'" }
>>   { "O3*" "O3'" }
>>   { "C2*" "C2'" }
>>   { "O2*" "O2'" }
>>   { "C1*" "C1'" }
>>   { "C5M" "C7"  }
>>   { "H1*" "H1'" }
>>   { "H2*1" "H2'" }
>>   { "H2*2" "H2''" }
>>   { "HO*2" "HO2'" }
>>   { "H2'1" "H2'" }
>>   { "H2'2" "H2''" }
>>   { "H3*" "H3'" }
>>   { "H4*" "H4'" }
>>   { "H5*1" "H5'" }
>>   { "H5*2" "H5''" }
>>   { "H5'1" "H5'" }
>>   { "H5'2" "H5''" }
>>   { "HO'2" "HO2'" }
>>   { "H5T"  "HO5'" }
>>   { "H3T"  "HO3'" }
>>   { "O1'" "O4'" }
>>   { "OA"  "OP1" }
>>   { "OB"  "OP2" }
>>   { "O1P" "OP1" }
>>   { "O2P" "OP2" }
>> }
>> 
>> #
>> # assume that most often proteins use HIE
>> #
>> NHIS = NHIE
>> HIS = HIE
>> CHIS = CHIE
> 
> loadoff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
> loadamberparams frcmod.opc
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.opc
Reading force field modification type file (frcmod)
Reading title:
Parameters for OPC water (JPCL, 2014, 5 (21), pp 3863–3871) 
(UNKNOWN ATOM TYPE: EP)
> loadamberparams frcmod.ionsjc_tip4pew
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip4pew
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP4P/EW water from Joung & Cheatham JPCB (2008)
> 
> m = loadpdb init.pdb
Loading PDB file: ./init.pdb
Enter zPdbReadScan from call depth  0.
Exit  zPdbReadScan from call depth  0.
Matching PDB residue names to LEaP variables.
(Residue 0: A5, Terminal/beginning, was not found in name map.)
(Residue 1: C3, Terminal/last, was not found in name map.)
Joining A5 - C3
  total atoms in file: 63
> 
> 
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.131155 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<H4' 9>
Warning: Close contact of 1.307451 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<C4' 8>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> solvatebox m OPCBOX 10.5 iso
  Solute vdw bounding box:              12.265 11.150 10.292
  Total bounding box for atom centers:  33.265 33.265 33.265
      (box expansion for 'iso' is  10.0%)
  Solvent unit box:                     18.865 18.478 19.006
The number of boxes:  x= 2  y= 2  z= 2
Adding box at: x=0  y=0  z=0
Center of solvent box is: 9.432422, 9.239054, 9.503120
Adding box at: x=0  y=0  z=1
Center of solvent box is: 9.432422, 9.239054, -9.503120
Adding box at: x=0  y=1  z=0
Center of solvent box is: 9.432422, -9.239054, 9.503120
Adding box at: x=0  y=1  z=1
Center of solvent box is: 9.432422, -9.239054, -9.503120
Adding box at: x=1  y=0  z=0
Center of solvent box is: -9.432422, 9.239054, 9.503120
Adding box at: x=1  y=0  z=1
Center of solvent box is: -9.432422, 9.239054, -9.503120
Adding box at: x=1  y=1  z=0
Center of solvent box is: -9.432422, -9.239054, 9.503120
Adding box at: x=1  y=1  z=1
Center of solvent box is: -9.432422, -9.239054, -9.503120
  Volume: 47132.626 A^3 
  Total mass 19506.248 amu,  Density 0.687 g/cc
  Added 1051 residues.
> quit
	Quit
log started: Sun Nov  1 20:53:03 2015

Log file: ./leap.log
>> #
>> # ----- leaprc for loading the ff12SB force field
>> # ----- NOTE: this is designed for PDB format 3!
>> #    Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA
>> #
>> #	load atom type hybridizations
>> #
>> addAtomTypes {
>> 	{ "H"   "H" "sp3" }
>> 	{ "HO"  "H" "sp3" }
>> 	{ "HS"  "H" "sp3" }
>> 	{ "H1"  "H" "sp3" }
>> 	{ "H2"  "H" "sp3" }
>> 	{ "H3"  "H" "sp3" }
>> 	{ "H4"  "H" "sp3" }
>> 	{ "H5"  "H" "sp3" }
>> 	{ "HW"  "H" "sp3" }
>> 	{ "HC"  "H" "sp3" }
>> 	{ "HA"  "H" "sp3" }
>> 	{ "HP"  "H" "sp3" }
>> 	{ "HZ"  "H" "sp3" }
>> 	{ "OH"  "O" "sp3" }
>> 	{ "OS"  "O" "sp3" }
>> 	{ "O"   "O" "sp2" }
>> 	{ "O2"  "O" "sp2" }
>> 	{ "OP"  "O" "sp2" }
>> 	{ "OW"  "O" "sp3" }
>> 	{ "CT"  "C" "sp3" }
>> 	{ "CX"  "C" "sp3" }
>> 	{ "C8"  "C" "sp3" }
>> 	{ "2C"  "C" "sp3" }
>> 	{ "3C"  "C" "sp3" }
>> 	{ "CH"  "C" "sp3" }
>> 	{ "CS"  "C" "sp2" }
>> 	{ "C"   "C" "sp2" }
>> 	{ "CO"   "C" "sp2" }
>> 	{ "C*"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CB"  "C" "sp2" }
>> 	{ "CC"  "C" "sp2" }
>> 	{ "CN"  "C" "sp2" }
>> 	{ "CM"  "C" "sp2" }
>> 	{ "CK"  "C" "sp2" }
>> 	{ "CQ"  "C" "sp2" }
>> 	{ "CD"  "C" "sp2" }
>> 	{ "C5"  "C" "sp2" }
>> 	{ "C4"  "C" "sp2" }
>> 	{ "CP"  "C" "sp2" }
>> 	{ "CI"  "C" "sp3" }
>> 	{ "CJ"  "C" "sp2" }
>> 	{ "CW"  "C" "sp2" }
>> 	{ "CV"  "C" "sp2" }
>> 	{ "CR"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CY"  "C" "sp2" }
>> 	{ "C0"  "Ca" "sp3" }
>> 	{ "MG"  "Mg" "sp3" }
>> 	{ "N"   "N" "sp2" }
>> 	{ "NA"  "N" "sp2" }
>> 	{ "N2"  "N" "sp2" }
>> 	{ "N*"  "N" "sp2" }
>> 	{ "NP"  "N" "sp2" }
>> 	{ "NQ"  "N" "sp2" }
>> 	{ "NB"  "N" "sp2" }
>> 	{ "NC"  "N" "sp2" }
>> 	{ "NT"  "N" "sp3" }
>> 	{ "NY"  "N" "sp2" }
>> 	{ "N3"  "N" "sp3" }
>> 	{ "S"   "S" "sp3" }
>> 	{ "SH"  "S" "sp3" }
>> 	{ "P"   "P" "sp3" }
>> 	{ "LP"  ""  "sp3" }
>> 	{ "EP"  ""  "sp3" }
>> 	{ "F"   "F" "sp3" }
>> 	{ "Cl"  "Cl" "sp3" }
>> 	{ "Br"  "Br" "sp3" }
>> 	{ "I"   "I"  "sp3" }
>> 	{ "F-"   "F" "sp3" }
>> 	{ "Cl-"  "Cl" "sp3" }
>> 	{ "Br-"  "Br" "sp3" }
>> 	{ "I-"   "I"  "sp3" }
>> 	{ "Li+"  "Li"  "sp3" }
>> 	{ "Na+"  "Na"  "sp3" }
>> 	{ "K+"  "K"  "sp3" }
>> 	{ "Rb+"  "Rb"  "sp3" }
>> 	{ "Cs+"  "Cs"  "sp3" }
>> 	{ "Mg+"  "Mg"  "sp3" }
>> # glycam
>> 	{ "OG"  "O" "sp3" }
>> 	{ "OL"  "O" "sp3" }
>> 	{ "AC"  "C" "sp3" }
>> 	{ "EC"  "C" "sp3" }
>> }
>> #
>> #	Load the main parameter set.
>> #
>> parm10 = loadamberparams parm10.dat
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
(UNKNOWN ATOM TYPE: Zn)
(UNKNOWN ATOM TYPE: EP)
>> frcmod12SB = loadamberparams frcmod.ff12SB
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff12SB
Reading force field modification type file (frcmod)
Reading title:
ff12SB protein backbone and sidechain parameters
>> #
>> #	Load main chain and terminating amino acid libraries, nucleic acids
>> #
>> loadOff amino12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/amino12.lib
Loading: ALA
Loading: ARG
Loading: ASH
Loading: ASN
Loading: ASP
Loading: CYM
Loading: CYS
Loading: CYX
Loading: GLH
Loading: GLN
Loading: GLU
Loading: GLY
Loading: HID
Loading: HIE
Loading: HIP
Loading: HYP
Loading: ILE
Loading: LEU
Loading: LYN
Loading: LYS
Loading: MET
Loading: PHE
Loading: PRO
Loading: SER
Loading: THR
Loading: TRP
Loading: TYR
Loading: VAL
>> loadOff aminoct12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminoct12.lib
Loading: CALA
Loading: CARG
Loading: CASN
Loading: CASP
Loading: CCYS
Loading: CCYX
Loading: CGLN
Loading: CGLU
Loading: CGLY
Loading: CHID
Loading: CHIE
Loading: CHIP
Loading: CHYP
Loading: CILE
Loading: CLEU
Loading: CLYS
Loading: CMET
Loading: CPHE
Loading: CPRO
Loading: CSER
Loading: CTHR
Loading: CTRP
Loading: CTYR
Loading: CVAL
Loading: NHE
Loading: NME
>> loadOff aminont12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminont12.lib
Loading: ACE
Loading: NALA
Loading: NARG
Loading: NASN
Loading: NASP
Loading: NCYS
Loading: NCYX
Loading: NGLN
Loading: NGLU
Loading: NGLY
Loading: NHID
Loading: NHIE
Loading: NHIP
Loading: NILE
Loading: NLEU
Loading: NLYS
Loading: NMET
Loading: NPHE
Loading: NPRO
Loading: NSER
Loading: NTHR
Loading: NTRP
Loading: NTYR
Loading: NVAL
>> loadOff nucleic12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/nucleic12.lib
Loading: A
Loading: A3
Loading: A5
Loading: AN
Loading: C
Loading: C3
Loading: C5
Loading: CN
Loading: DA
Loading: DA3
Loading: DA5
Loading: DAN
Loading: DC
Loading: DC3
Loading: DC5
Loading: DCN
Loading: DG
Loading: DG3
Loading: DG5
Loading: DGN
Loading: DT
Loading: DT3
Loading: DT5
Loading: DTN
Loading: G
Loading: G3
Loading: G5
Loading: GN
Loading: OHE
Loading: U
Loading: U3
Loading: U5
Loading: UN
>> #
>> #       Load water and ions
>> # 
>> loadOff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
>> loadOff solvents.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: MEOHBOX
Loading: NMABOX
Loading: OPC
Loading: OPCBOX
Loading: PL3
Loading: POL3BOX
Loading: QSPCFWBOX
Loading: SPC
Loading: SPCBOX
Loading: SPCFWBOX
Loading: SPF
Loading: SPG
Loading: T4E
Loading: TIP3PBOX
Loading: TIP3PFBOX
Loading: TIP4PBOX
Loading: TIP4PEWBOX
Loading: TIP5PBOX
Loading: TP3
Loading: TP4
Loading: TP5
Loading: TPF
>> HOH = TP3
>> WAT = TP3
>> 
>> #
>> #	Define the PDB name map for the amino acids and nucleic acids
>> #     (note: no NHYP!  use neutral form for now)
>> #
>> addPdbResMap {
>>   { 0 "HYP" "HYP"  } { 1 "HYP" "CHYP" }
>>   { 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
>>   { 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
>>   { 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
>>   { 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
>>   { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
>>   { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
>>   { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
>>   { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
>>   { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
>>   { 0 "HID" "NHID" } { 1 "HID" "CHID" }
>>   { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
>>   { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
>>   { 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
>>   { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
>>   { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
>>   { 0 "MET" "NMET" } { 1 "MET" "CMET" }
>>   { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
>>   { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
>>   { 0 "SER" "NSER" } { 1 "SER" "CSER" }
>>   { 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
>>   { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
>>   { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
>>   { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
>>   { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
>>   { 0 "G" "G5"  } { 1 "G" "G3"  } 
>>   { 0 "A" "A5"  } { 1 "A" "A3"  } 
>>   { 0 "C" "C5"  } { 1 "C" "C3"  } 
>>   { 0 "U" "U5"  } { 1 "U" "U3"  } 
>>   { 0 "DG" "DG5"  } { 1 "DG" "DG3"  }  
>>   { 0 "DA" "DA5"  } { 1 "DA" "DA3"  }  
>>   { 0 "DC" "DC5"  } { 1 "DC" "DC3"  }  
>>   { 0 "DT" "DT5"  } { 1 "DT" "DT3"  }  
>> #  some old Amber residue names for RNA:
>>   { 0  "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" }
>>   { 0  "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" }
>>   { 0  "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" }
>>   { 0  "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" }
>> #  some really old Amber residue names, assuming DNA:
>>   { 0 "GUA" "DG5"  } { 1 "GUA" "DG3"  } { "GUA" "DG" }
>>   { 0 "ADE" "DA5"  } { 1 "ADE" "DA3"  } { "ADE" "DA" }
>>   { 0 "CYT" "DC5"  } { 1 "CYT" "DC3"  } { "CYT" "DC" }
>>   { 0 "THY" "DT5"  } { 1 "THY" "DT3"  } { "THY" "DT" }
>> #  uncomment out the following if you have this old style RNA files:
>> # { 0 "GUA" "G5"  } { 1 "GUA" "G3"  } { "GUA" "G" }
>> # { 0 "ADE" "A5"  } { 1 "ADE" "A3"  } { "ADE" "A" }
>> # { 0 "CYT" "C5"  } { 1 "CYT" "C3"  } { "CYT" "C" }
>> # { 0 "URA" "R5"  } { 1 "URA" "R3"  } { "URA" "R" }
>> 
>> }
>> 
>> #  try to be good about reading in really old atom names as well:
>> addPdbAtomMap {
>>   { "O5*" "O5'" }
>>   { "C5*" "C5'" }
>>   { "C4*" "C4'" }
>>   { "O4*" "O4'" }
>>   { "C3*" "C3'" }
>>   { "O3*" "O3'" }
>>   { "C2*" "C2'" }
>>   { "O2*" "O2'" }
>>   { "C1*" "C1'" }
>>   { "C5M" "C7"  }
>>   { "H1*" "H1'" }
>>   { "H2*1" "H2'" }
>>   { "H2*2" "H2''" }
>>   { "HO*2" "HO2'" }
>>   { "H2'1" "H2'" }
>>   { "H2'2" "H2''" }
>>   { "H3*" "H3'" }
>>   { "H4*" "H4'" }
>>   { "H5*1" "H5'" }
>>   { "H5*2" "H5''" }
>>   { "H5'1" "H5'" }
>>   { "H5'2" "H5''" }
>>   { "HO'2" "HO2'" }
>>   { "H5T"  "HO5'" }
>>   { "H3T"  "HO3'" }
>>   { "O1'" "O4'" }
>>   { "OA"  "OP1" }
>>   { "OB"  "OP2" }
>>   { "O1P" "OP1" }
>>   { "O2P" "OP2" }
>> }
>> 
>> #
>> # assume that most often proteins use HIE
>> #
>> NHIS = NHIE
>> HIS = HIE
>> CHIS = CHIE
> 
> loadoff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
> loadamberparams frcmod.opc
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.opc
Reading force field modification type file (frcmod)
Reading title:
Parameters for OPC water (JPCL, 2014, 5 (21), pp 3863–3871) 
(UNKNOWN ATOM TYPE: EP)
> loadamberparams frcmod.ionsjc_tip4pew
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip4pew
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP4P/EW water from Joung & Cheatham JPCB (2008)
> 
> m = loadpdb init.pdb
Loading PDB file: ./init.pdb
Enter zPdbReadScan from call depth  0.
Exit  zPdbReadScan from call depth  0.
Matching PDB residue names to LEaP variables.
(Residue 0: A5, Terminal/beginning, was not found in name map.)
(Residue 1: C3, Terminal/last, was not found in name map.)
Joining A5 - C3
  total atoms in file: 63
> 
> 
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.131155 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<H4' 9>
Warning: Close contact of 1.307451 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<C4' 8>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> solvatebox m OPCBOX 10.6 iso
  Solute vdw bounding box:              12.265 11.150 10.292
  Total bounding box for atom centers:  33.465 33.465 33.465
      (box expansion for 'iso' is   9.9%)
  Solvent unit box:                     18.865 18.478 19.006
The number of boxes:  x= 2  y= 2  z= 2
Adding box at: x=0  y=0  z=0
Center of solvent box is: 9.432422, 9.239054, 9.503120
Adding box at: x=0  y=0  z=1
Center of solvent box is: 9.432422, 9.239054, -9.503120
Adding box at: x=0  y=1  z=0
Center of solvent box is: 9.432422, -9.239054, 9.503120
Adding box at: x=0  y=1  z=1
Center of solvent box is: 9.432422, -9.239054, -9.503120
Adding box at: x=1  y=0  z=0
Center of solvent box is: -9.432422, 9.239054, 9.503120
Adding box at: x=1  y=0  z=1
Center of solvent box is: -9.432422, 9.239054, -9.503120
Adding box at: x=1  y=1  z=0
Center of solvent box is: -9.432422, -9.239054, 9.503120
Adding box at: x=1  y=1  z=1
Center of solvent box is: -9.432422, -9.239054, -9.503120
  Volume: 47135.242 A^3 
  Total mass 19830.536 amu,  Density 0.699 g/cc
  Added 1069 residues.
> quit
	Quit
log started: Sun Nov  1 20:53:03 2015

Log file: ./leap.log
>> #
>> # ----- leaprc for loading the ff12SB force field
>> # ----- NOTE: this is designed for PDB format 3!
>> #    Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA
>> #
>> #	load atom type hybridizations
>> #
>> addAtomTypes {
>> 	{ "H"   "H" "sp3" }
>> 	{ "HO"  "H" "sp3" }
>> 	{ "HS"  "H" "sp3" }
>> 	{ "H1"  "H" "sp3" }
>> 	{ "H2"  "H" "sp3" }
>> 	{ "H3"  "H" "sp3" }
>> 	{ "H4"  "H" "sp3" }
>> 	{ "H5"  "H" "sp3" }
>> 	{ "HW"  "H" "sp3" }
>> 	{ "HC"  "H" "sp3" }
>> 	{ "HA"  "H" "sp3" }
>> 	{ "HP"  "H" "sp3" }
>> 	{ "HZ"  "H" "sp3" }
>> 	{ "OH"  "O" "sp3" }
>> 	{ "OS"  "O" "sp3" }
>> 	{ "O"   "O" "sp2" }
>> 	{ "O2"  "O" "sp2" }
>> 	{ "OP"  "O" "sp2" }
>> 	{ "OW"  "O" "sp3" }
>> 	{ "CT"  "C" "sp3" }
>> 	{ "CX"  "C" "sp3" }
>> 	{ "C8"  "C" "sp3" }
>> 	{ "2C"  "C" "sp3" }
>> 	{ "3C"  "C" "sp3" }
>> 	{ "CH"  "C" "sp3" }
>> 	{ "CS"  "C" "sp2" }
>> 	{ "C"   "C" "sp2" }
>> 	{ "CO"   "C" "sp2" }
>> 	{ "C*"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CB"  "C" "sp2" }
>> 	{ "CC"  "C" "sp2" }
>> 	{ "CN"  "C" "sp2" }
>> 	{ "CM"  "C" "sp2" }
>> 	{ "CK"  "C" "sp2" }
>> 	{ "CQ"  "C" "sp2" }
>> 	{ "CD"  "C" "sp2" }
>> 	{ "C5"  "C" "sp2" }
>> 	{ "C4"  "C" "sp2" }
>> 	{ "CP"  "C" "sp2" }
>> 	{ "CI"  "C" "sp3" }
>> 	{ "CJ"  "C" "sp2" }
>> 	{ "CW"  "C" "sp2" }
>> 	{ "CV"  "C" "sp2" }
>> 	{ "CR"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CY"  "C" "sp2" }
>> 	{ "C0"  "Ca" "sp3" }
>> 	{ "MG"  "Mg" "sp3" }
>> 	{ "N"   "N" "sp2" }
>> 	{ "NA"  "N" "sp2" }
>> 	{ "N2"  "N" "sp2" }
>> 	{ "N*"  "N" "sp2" }
>> 	{ "NP"  "N" "sp2" }
>> 	{ "NQ"  "N" "sp2" }
>> 	{ "NB"  "N" "sp2" }
>> 	{ "NC"  "N" "sp2" }
>> 	{ "NT"  "N" "sp3" }
>> 	{ "NY"  "N" "sp2" }
>> 	{ "N3"  "N" "sp3" }
>> 	{ "S"   "S" "sp3" }
>> 	{ "SH"  "S" "sp3" }
>> 	{ "P"   "P" "sp3" }
>> 	{ "LP"  ""  "sp3" }
>> 	{ "EP"  ""  "sp3" }
>> 	{ "F"   "F" "sp3" }
>> 	{ "Cl"  "Cl" "sp3" }
>> 	{ "Br"  "Br" "sp3" }
>> 	{ "I"   "I"  "sp3" }
>> 	{ "F-"   "F" "sp3" }
>> 	{ "Cl-"  "Cl" "sp3" }
>> 	{ "Br-"  "Br" "sp3" }
>> 	{ "I-"   "I"  "sp3" }
>> 	{ "Li+"  "Li"  "sp3" }
>> 	{ "Na+"  "Na"  "sp3" }
>> 	{ "K+"  "K"  "sp3" }
>> 	{ "Rb+"  "Rb"  "sp3" }
>> 	{ "Cs+"  "Cs"  "sp3" }
>> 	{ "Mg+"  "Mg"  "sp3" }
>> # glycam
>> 	{ "OG"  "O" "sp3" }
>> 	{ "OL"  "O" "sp3" }
>> 	{ "AC"  "C" "sp3" }
>> 	{ "EC"  "C" "sp3" }
>> }
>> #
>> #	Load the main parameter set.
>> #
>> parm10 = loadamberparams parm10.dat
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
(UNKNOWN ATOM TYPE: Zn)
(UNKNOWN ATOM TYPE: EP)
>> frcmod12SB = loadamberparams frcmod.ff12SB
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff12SB
Reading force field modification type file (frcmod)
Reading title:
ff12SB protein backbone and sidechain parameters
>> #
>> #	Load main chain and terminating amino acid libraries, nucleic acids
>> #
>> loadOff amino12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/amino12.lib
Loading: ALA
Loading: ARG
Loading: ASH
Loading: ASN
Loading: ASP
Loading: CYM
Loading: CYS
Loading: CYX
Loading: GLH
Loading: GLN
Loading: GLU
Loading: GLY
Loading: HID
Loading: HIE
Loading: HIP
Loading: HYP
Loading: ILE
Loading: LEU
Loading: LYN
Loading: LYS
Loading: MET
Loading: PHE
Loading: PRO
Loading: SER
Loading: THR
Loading: TRP
Loading: TYR
Loading: VAL
>> loadOff aminoct12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminoct12.lib
Loading: CALA
Loading: CARG
Loading: CASN
Loading: CASP
Loading: CCYS
Loading: CCYX
Loading: CGLN
Loading: CGLU
Loading: CGLY
Loading: CHID
Loading: CHIE
Loading: CHIP
Loading: CHYP
Loading: CILE
Loading: CLEU
Loading: CLYS
Loading: CMET
Loading: CPHE
Loading: CPRO
Loading: CSER
Loading: CTHR
Loading: CTRP
Loading: CTYR
Loading: CVAL
Loading: NHE
Loading: NME
>> loadOff aminont12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminont12.lib
Loading: ACE
Loading: NALA
Loading: NARG
Loading: NASN
Loading: NASP
Loading: NCYS
Loading: NCYX
Loading: NGLN
Loading: NGLU
Loading: NGLY
Loading: NHID
Loading: NHIE
Loading: NHIP
Loading: NILE
Loading: NLEU
Loading: NLYS
Loading: NMET
Loading: NPHE
Loading: NPRO
Loading: NSER
Loading: NTHR
Loading: NTRP
Loading: NTYR
Loading: NVAL
>> loadOff nucleic12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/nucleic12.lib
Loading: A
Loading: A3
Loading: A5
Loading: AN
Loading: C
Loading: C3
Loading: C5
Loading: CN
Loading: DA
Loading: DA3
Loading: DA5
Loading: DAN
Loading: DC
Loading: DC3
Loading: DC5
Loading: DCN
Loading: DG
Loading: DG3
Loading: DG5
Loading: DGN
Loading: DT
Loading: DT3
Loading: DT5
Loading: DTN
Loading: G
Loading: G3
Loading: G5
Loading: GN
Loading: OHE
Loading: U
Loading: U3
Loading: U5
Loading: UN
>> #
>> #       Load water and ions
>> # 
>> loadOff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
>> loadOff solvents.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: MEOHBOX
Loading: NMABOX
Loading: OPC
Loading: OPCBOX
Loading: PL3
Loading: POL3BOX
Loading: QSPCFWBOX
Loading: SPC
Loading: SPCBOX
Loading: SPCFWBOX
Loading: SPF
Loading: SPG
Loading: T4E
Loading: TIP3PBOX
Loading: TIP3PFBOX
Loading: TIP4PBOX
Loading: TIP4PEWBOX
Loading: TIP5PBOX
Loading: TP3
Loading: TP4
Loading: TP5
Loading: TPF
>> HOH = TP3
>> WAT = TP3
>> 
>> #
>> #	Define the PDB name map for the amino acids and nucleic acids
>> #     (note: no NHYP!  use neutral form for now)
>> #
>> addPdbResMap {
>>   { 0 "HYP" "HYP"  } { 1 "HYP" "CHYP" }
>>   { 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
>>   { 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
>>   { 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
>>   { 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
>>   { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
>>   { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
>>   { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
>>   { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
>>   { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
>>   { 0 "HID" "NHID" } { 1 "HID" "CHID" }
>>   { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
>>   { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
>>   { 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
>>   { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
>>   { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
>>   { 0 "MET" "NMET" } { 1 "MET" "CMET" }
>>   { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
>>   { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
>>   { 0 "SER" "NSER" } { 1 "SER" "CSER" }
>>   { 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
>>   { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
>>   { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
>>   { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
>>   { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
>>   { 0 "G" "G5"  } { 1 "G" "G3"  } 
>>   { 0 "A" "A5"  } { 1 "A" "A3"  } 
>>   { 0 "C" "C5"  } { 1 "C" "C3"  } 
>>   { 0 "U" "U5"  } { 1 "U" "U3"  } 
>>   { 0 "DG" "DG5"  } { 1 "DG" "DG3"  }  
>>   { 0 "DA" "DA5"  } { 1 "DA" "DA3"  }  
>>   { 0 "DC" "DC5"  } { 1 "DC" "DC3"  }  
>>   { 0 "DT" "DT5"  } { 1 "DT" "DT3"  }  
>> #  some old Amber residue names for RNA:
>>   { 0  "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" }
>>   { 0  "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" }
>>   { 0  "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" }
>>   { 0  "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" }
>> #  some really old Amber residue names, assuming DNA:
>>   { 0 "GUA" "DG5"  } { 1 "GUA" "DG3"  } { "GUA" "DG" }
>>   { 0 "ADE" "DA5"  } { 1 "ADE" "DA3"  } { "ADE" "DA" }
>>   { 0 "CYT" "DC5"  } { 1 "CYT" "DC3"  } { "CYT" "DC" }
>>   { 0 "THY" "DT5"  } { 1 "THY" "DT3"  } { "THY" "DT" }
>> #  uncomment out the following if you have this old style RNA files:
>> # { 0 "GUA" "G5"  } { 1 "GUA" "G3"  } { "GUA" "G" }
>> # { 0 "ADE" "A5"  } { 1 "ADE" "A3"  } { "ADE" "A" }
>> # { 0 "CYT" "C5"  } { 1 "CYT" "C3"  } { "CYT" "C" }
>> # { 0 "URA" "R5"  } { 1 "URA" "R3"  } { "URA" "R" }
>> 
>> }
>> 
>> #  try to be good about reading in really old atom names as well:
>> addPdbAtomMap {
>>   { "O5*" "O5'" }
>>   { "C5*" "C5'" }
>>   { "C4*" "C4'" }
>>   { "O4*" "O4'" }
>>   { "C3*" "C3'" }
>>   { "O3*" "O3'" }
>>   { "C2*" "C2'" }
>>   { "O2*" "O2'" }
>>   { "C1*" "C1'" }
>>   { "C5M" "C7"  }
>>   { "H1*" "H1'" }
>>   { "H2*1" "H2'" }
>>   { "H2*2" "H2''" }
>>   { "HO*2" "HO2'" }
>>   { "H2'1" "H2'" }
>>   { "H2'2" "H2''" }
>>   { "H3*" "H3'" }
>>   { "H4*" "H4'" }
>>   { "H5*1" "H5'" }
>>   { "H5*2" "H5''" }
>>   { "H5'1" "H5'" }
>>   { "H5'2" "H5''" }
>>   { "HO'2" "HO2'" }
>>   { "H5T"  "HO5'" }
>>   { "H3T"  "HO3'" }
>>   { "O1'" "O4'" }
>>   { "OA"  "OP1" }
>>   { "OB"  "OP2" }
>>   { "O1P" "OP1" }
>>   { "O2P" "OP2" }
>> }
>> 
>> #
>> # assume that most often proteins use HIE
>> #
>> NHIS = NHIE
>> HIS = HIE
>> CHIS = CHIE
> 
> loadoff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
> loadamberparams frcmod.opc
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.opc
Reading force field modification type file (frcmod)
Reading title:
Parameters for OPC water (JPCL, 2014, 5 (21), pp 3863–3871) 
(UNKNOWN ATOM TYPE: EP)
> loadamberparams frcmod.ionsjc_tip4pew
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip4pew
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP4P/EW water from Joung & Cheatham JPCB (2008)
> 
> m = loadpdb init.pdb
Loading PDB file: ./init.pdb
Enter zPdbReadScan from call depth  0.
Exit  zPdbReadScan from call depth  0.
Matching PDB residue names to LEaP variables.
(Residue 0: A5, Terminal/beginning, was not found in name map.)
(Residue 1: C3, Terminal/last, was not found in name map.)
Joining A5 - C3
  total atoms in file: 63
> 
> 
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.131155 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<H4' 9>
Warning: Close contact of 1.307451 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<C4' 8>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> solvatebox m OPCBOX 10.7 iso
  Solute vdw bounding box:              12.265 11.150 10.292
  Total bounding box for atom centers:  33.665 33.665 33.665
      (box expansion for 'iso' is   9.9%)
  Solvent unit box:                     18.865 18.478 19.006
The number of boxes:  x= 2  y= 2  z= 2
Adding box at: x=0  y=0  z=0
Center of solvent box is: 9.432422, 9.239054, 9.503120
Adding box at: x=0  y=0  z=1
Center of solvent box is: 9.432422, 9.239054, -9.503120
Adding box at: x=0  y=1  z=0
Center of solvent box is: 9.432422, -9.239054, 9.503120
Adding box at: x=0  y=1  z=1
Center of solvent box is: 9.432422, -9.239054, -9.503120
Adding box at: x=1  y=0  z=0
Center of solvent box is: -9.432422, 9.239054, 9.503120
Adding box at: x=1  y=0  z=1
Center of solvent box is: -9.432422, 9.239054, -9.503120
Adding box at: x=1  y=1  z=0
Center of solvent box is: -9.432422, -9.239054, 9.503120
Adding box at: x=1  y=1  z=1
Center of solvent box is: -9.432422, -9.239054, -9.503120
  Volume: 49083.880 A^3 
  Total mass 20280.936 amu,  Density 0.686 g/cc
  Added 1094 residues.
> quit
	Quit
log started: Sun Nov  1 20:53:03 2015

Log file: ./leap.log
>> #
>> # ----- leaprc for loading the ff12SB force field
>> # ----- NOTE: this is designed for PDB format 3!
>> #    Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA
>> #
>> #	load atom type hybridizations
>> #
>> addAtomTypes {
>> 	{ "H"   "H" "sp3" }
>> 	{ "HO"  "H" "sp3" }
>> 	{ "HS"  "H" "sp3" }
>> 	{ "H1"  "H" "sp3" }
>> 	{ "H2"  "H" "sp3" }
>> 	{ "H3"  "H" "sp3" }
>> 	{ "H4"  "H" "sp3" }
>> 	{ "H5"  "H" "sp3" }
>> 	{ "HW"  "H" "sp3" }
>> 	{ "HC"  "H" "sp3" }
>> 	{ "HA"  "H" "sp3" }
>> 	{ "HP"  "H" "sp3" }
>> 	{ "HZ"  "H" "sp3" }
>> 	{ "OH"  "O" "sp3" }
>> 	{ "OS"  "O" "sp3" }
>> 	{ "O"   "O" "sp2" }
>> 	{ "O2"  "O" "sp2" }
>> 	{ "OP"  "O" "sp2" }
>> 	{ "OW"  "O" "sp3" }
>> 	{ "CT"  "C" "sp3" }
>> 	{ "CX"  "C" "sp3" }
>> 	{ "C8"  "C" "sp3" }
>> 	{ "2C"  "C" "sp3" }
>> 	{ "3C"  "C" "sp3" }
>> 	{ "CH"  "C" "sp3" }
>> 	{ "CS"  "C" "sp2" }
>> 	{ "C"   "C" "sp2" }
>> 	{ "CO"   "C" "sp2" }
>> 	{ "C*"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CB"  "C" "sp2" }
>> 	{ "CC"  "C" "sp2" }
>> 	{ "CN"  "C" "sp2" }
>> 	{ "CM"  "C" "sp2" }
>> 	{ "CK"  "C" "sp2" }
>> 	{ "CQ"  "C" "sp2" }
>> 	{ "CD"  "C" "sp2" }
>> 	{ "C5"  "C" "sp2" }
>> 	{ "C4"  "C" "sp2" }
>> 	{ "CP"  "C" "sp2" }
>> 	{ "CI"  "C" "sp3" }
>> 	{ "CJ"  "C" "sp2" }
>> 	{ "CW"  "C" "sp2" }
>> 	{ "CV"  "C" "sp2" }
>> 	{ "CR"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CY"  "C" "sp2" }
>> 	{ "C0"  "Ca" "sp3" }
>> 	{ "MG"  "Mg" "sp3" }
>> 	{ "N"   "N" "sp2" }
>> 	{ "NA"  "N" "sp2" }
>> 	{ "N2"  "N" "sp2" }
>> 	{ "N*"  "N" "sp2" }
>> 	{ "NP"  "N" "sp2" }
>> 	{ "NQ"  "N" "sp2" }
>> 	{ "NB"  "N" "sp2" }
>> 	{ "NC"  "N" "sp2" }
>> 	{ "NT"  "N" "sp3" }
>> 	{ "NY"  "N" "sp2" }
>> 	{ "N3"  "N" "sp3" }
>> 	{ "S"   "S" "sp3" }
>> 	{ "SH"  "S" "sp3" }
>> 	{ "P"   "P" "sp3" }
>> 	{ "LP"  ""  "sp3" }
>> 	{ "EP"  ""  "sp3" }
>> 	{ "F"   "F" "sp3" }
>> 	{ "Cl"  "Cl" "sp3" }
>> 	{ "Br"  "Br" "sp3" }
>> 	{ "I"   "I"  "sp3" }
>> 	{ "F-"   "F" "sp3" }
>> 	{ "Cl-"  "Cl" "sp3" }
>> 	{ "Br-"  "Br" "sp3" }
>> 	{ "I-"   "I"  "sp3" }
>> 	{ "Li+"  "Li"  "sp3" }
>> 	{ "Na+"  "Na"  "sp3" }
>> 	{ "K+"  "K"  "sp3" }
>> 	{ "Rb+"  "Rb"  "sp3" }
>> 	{ "Cs+"  "Cs"  "sp3" }
>> 	{ "Mg+"  "Mg"  "sp3" }
>> # glycam
>> 	{ "OG"  "O" "sp3" }
>> 	{ "OL"  "O" "sp3" }
>> 	{ "AC"  "C" "sp3" }
>> 	{ "EC"  "C" "sp3" }
>> }
>> #
>> #	Load the main parameter set.
>> #
>> parm10 = loadamberparams parm10.dat
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
(UNKNOWN ATOM TYPE: Zn)
(UNKNOWN ATOM TYPE: EP)
>> frcmod12SB = loadamberparams frcmod.ff12SB
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff12SB
Reading force field modification type file (frcmod)
Reading title:
ff12SB protein backbone and sidechain parameters
>> #
>> #	Load main chain and terminating amino acid libraries, nucleic acids
>> #
>> loadOff amino12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/amino12.lib
Loading: ALA
Loading: ARG
Loading: ASH
Loading: ASN
Loading: ASP
Loading: CYM
Loading: CYS
Loading: CYX
Loading: GLH
Loading: GLN
Loading: GLU
Loading: GLY
Loading: HID
Loading: HIE
Loading: HIP
Loading: HYP
Loading: ILE
Loading: LEU
Loading: LYN
Loading: LYS
Loading: MET
Loading: PHE
Loading: PRO
Loading: SER
Loading: THR
Loading: TRP
Loading: TYR
Loading: VAL
>> loadOff aminoct12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminoct12.lib
Loading: CALA
Loading: CARG
Loading: CASN
Loading: CASP
Loading: CCYS
Loading: CCYX
Loading: CGLN
Loading: CGLU
Loading: CGLY
Loading: CHID
Loading: CHIE
Loading: CHIP
Loading: CHYP
Loading: CILE
Loading: CLEU
Loading: CLYS
Loading: CMET
Loading: CPHE
Loading: CPRO
Loading: CSER
Loading: CTHR
Loading: CTRP
Loading: CTYR
Loading: CVAL
Loading: NHE
Loading: NME
>> loadOff aminont12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminont12.lib
Loading: ACE
Loading: NALA
Loading: NARG
Loading: NASN
Loading: NASP
Loading: NCYS
Loading: NCYX
Loading: NGLN
Loading: NGLU
Loading: NGLY
Loading: NHID
Loading: NHIE
Loading: NHIP
Loading: NILE
Loading: NLEU
Loading: NLYS
Loading: NMET
Loading: NPHE
Loading: NPRO
Loading: NSER
Loading: NTHR
Loading: NTRP
Loading: NTYR
Loading: NVAL
>> loadOff nucleic12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/nucleic12.lib
Loading: A
Loading: A3
Loading: A5
Loading: AN
Loading: C
Loading: C3
Loading: C5
Loading: CN
Loading: DA
Loading: DA3
Loading: DA5
Loading: DAN
Loading: DC
Loading: DC3
Loading: DC5
Loading: DCN
Loading: DG
Loading: DG3
Loading: DG5
Loading: DGN
Loading: DT
Loading: DT3
Loading: DT5
Loading: DTN
Loading: G
Loading: G3
Loading: G5
Loading: GN
Loading: OHE
Loading: U
Loading: U3
Loading: U5
Loading: UN
>> #
>> #       Load water and ions
>> # 
>> loadOff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
>> loadOff solvents.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: MEOHBOX
Loading: NMABOX
Loading: OPC
Loading: OPCBOX
Loading: PL3
Loading: POL3BOX
Loading: QSPCFWBOX
Loading: SPC
Loading: SPCBOX
Loading: SPCFWBOX
Loading: SPF
Loading: SPG
Loading: T4E
Loading: TIP3PBOX
Loading: TIP3PFBOX
Loading: TIP4PBOX
Loading: TIP4PEWBOX
Loading: TIP5PBOX
Loading: TP3
Loading: TP4
Loading: TP5
Loading: TPF
>> HOH = TP3
>> WAT = TP3
>> 
>> #
>> #	Define the PDB name map for the amino acids and nucleic acids
>> #     (note: no NHYP!  use neutral form for now)
>> #
>> addPdbResMap {
>>   { 0 "HYP" "HYP"  } { 1 "HYP" "CHYP" }
>>   { 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
>>   { 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
>>   { 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
>>   { 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
>>   { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
>>   { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
>>   { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
>>   { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
>>   { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
>>   { 0 "HID" "NHID" } { 1 "HID" "CHID" }
>>   { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
>>   { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
>>   { 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
>>   { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
>>   { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
>>   { 0 "MET" "NMET" } { 1 "MET" "CMET" }
>>   { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
>>   { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
>>   { 0 "SER" "NSER" } { 1 "SER" "CSER" }
>>   { 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
>>   { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
>>   { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
>>   { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
>>   { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
>>   { 0 "G" "G5"  } { 1 "G" "G3"  } 
>>   { 0 "A" "A5"  } { 1 "A" "A3"  } 
>>   { 0 "C" "C5"  } { 1 "C" "C3"  } 
>>   { 0 "U" "U5"  } { 1 "U" "U3"  } 
>>   { 0 "DG" "DG5"  } { 1 "DG" "DG3"  }  
>>   { 0 "DA" "DA5"  } { 1 "DA" "DA3"  }  
>>   { 0 "DC" "DC5"  } { 1 "DC" "DC3"  }  
>>   { 0 "DT" "DT5"  } { 1 "DT" "DT3"  }  
>> #  some old Amber residue names for RNA:
>>   { 0  "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" }
>>   { 0  "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" }
>>   { 0  "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" }
>>   { 0  "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" }
>> #  some really old Amber residue names, assuming DNA:
>>   { 0 "GUA" "DG5"  } { 1 "GUA" "DG3"  } { "GUA" "DG" }
>>   { 0 "ADE" "DA5"  } { 1 "ADE" "DA3"  } { "ADE" "DA" }
>>   { 0 "CYT" "DC5"  } { 1 "CYT" "DC3"  } { "CYT" "DC" }
>>   { 0 "THY" "DT5"  } { 1 "THY" "DT3"  } { "THY" "DT" }
>> #  uncomment out the following if you have this old style RNA files:
>> # { 0 "GUA" "G5"  } { 1 "GUA" "G3"  } { "GUA" "G" }
>> # { 0 "ADE" "A5"  } { 1 "ADE" "A3"  } { "ADE" "A" }
>> # { 0 "CYT" "C5"  } { 1 "CYT" "C3"  } { "CYT" "C" }
>> # { 0 "URA" "R5"  } { 1 "URA" "R3"  } { "URA" "R" }
>> 
>> }
>> 
>> #  try to be good about reading in really old atom names as well:
>> addPdbAtomMap {
>>   { "O5*" "O5'" }
>>   { "C5*" "C5'" }
>>   { "C4*" "C4'" }
>>   { "O4*" "O4'" }
>>   { "C3*" "C3'" }
>>   { "O3*" "O3'" }
>>   { "C2*" "C2'" }
>>   { "O2*" "O2'" }
>>   { "C1*" "C1'" }
>>   { "C5M" "C7"  }
>>   { "H1*" "H1'" }
>>   { "H2*1" "H2'" }
>>   { "H2*2" "H2''" }
>>   { "HO*2" "HO2'" }
>>   { "H2'1" "H2'" }
>>   { "H2'2" "H2''" }
>>   { "H3*" "H3'" }
>>   { "H4*" "H4'" }
>>   { "H5*1" "H5'" }
>>   { "H5*2" "H5''" }
>>   { "H5'1" "H5'" }
>>   { "H5'2" "H5''" }
>>   { "HO'2" "HO2'" }
>>   { "H5T"  "HO5'" }
>>   { "H3T"  "HO3'" }
>>   { "O1'" "O4'" }
>>   { "OA"  "OP1" }
>>   { "OB"  "OP2" }
>>   { "O1P" "OP1" }
>>   { "O2P" "OP2" }
>> }
>> 
>> #
>> # assume that most often proteins use HIE
>> #
>> NHIS = NHIE
>> HIS = HIE
>> CHIS = CHIE
> 
> loadoff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
> loadamberparams frcmod.opc
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.opc
Reading force field modification type file (frcmod)
Reading title:
Parameters for OPC water (JPCL, 2014, 5 (21), pp 3863–3871) 
(UNKNOWN ATOM TYPE: EP)
> loadamberparams frcmod.ionsjc_tip4pew
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip4pew
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP4P/EW water from Joung & Cheatham JPCB (2008)
> 
> m = loadpdb init.pdb
Loading PDB file: ./init.pdb
Enter zPdbReadScan from call depth  0.
Exit  zPdbReadScan from call depth  0.
Matching PDB residue names to LEaP variables.
(Residue 0: A5, Terminal/beginning, was not found in name map.)
(Residue 1: C3, Terminal/last, was not found in name map.)
Joining A5 - C3
  total atoms in file: 63
> 
> 
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.131155 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<H4' 9>
Warning: Close contact of 1.307451 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<C4' 8>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> solvatebox m OPCBOX 10.65 iso
  Solute vdw bounding box:              12.265 11.150 10.292
  Total bounding box for atom centers:  33.565 33.565 33.565
      (box expansion for 'iso' is   9.9%)
  Solvent unit box:                     18.865 18.478 19.006
The number of boxes:  x= 2  y= 2  z= 2
Adding box at: x=0  y=0  z=0
Center of solvent box is: 9.432422, 9.239054, 9.503120
Adding box at: x=0  y=0  z=1
Center of solvent box is: 9.432422, 9.239054, -9.503120
Adding box at: x=0  y=1  z=0
Center of solvent box is: 9.432422, -9.239054, 9.503120
Adding box at: x=0  y=1  z=1
Center of solvent box is: 9.432422, -9.239054, -9.503120
Adding box at: x=1  y=0  z=0
Center of solvent box is: -9.432422, 9.239054, 9.503120
Adding box at: x=1  y=0  z=1
Center of solvent box is: -9.432422, 9.239054, -9.503120
Adding box at: x=1  y=1  z=0
Center of solvent box is: -9.432422, -9.239054, 9.503120
Adding box at: x=1  y=1  z=1
Center of solvent box is: -9.432422, -9.239054, -9.503120
  Volume: 48540.290 A^3 
  Total mass 19992.680 amu,  Density 0.684 g/cc
  Added 1078 residues.
> quit
	Quit
log started: Sun Nov  1 20:53:03 2015

Log file: ./leap.log
>> #
>> # ----- leaprc for loading the ff12SB force field
>> # ----- NOTE: this is designed for PDB format 3!
>> #    Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA
>> #
>> #	load atom type hybridizations
>> #
>> addAtomTypes {
>> 	{ "H"   "H" "sp3" }
>> 	{ "HO"  "H" "sp3" }
>> 	{ "HS"  "H" "sp3" }
>> 	{ "H1"  "H" "sp3" }
>> 	{ "H2"  "H" "sp3" }
>> 	{ "H3"  "H" "sp3" }
>> 	{ "H4"  "H" "sp3" }
>> 	{ "H5"  "H" "sp3" }
>> 	{ "HW"  "H" "sp3" }
>> 	{ "HC"  "H" "sp3" }
>> 	{ "HA"  "H" "sp3" }
>> 	{ "HP"  "H" "sp3" }
>> 	{ "HZ"  "H" "sp3" }
>> 	{ "OH"  "O" "sp3" }
>> 	{ "OS"  "O" "sp3" }
>> 	{ "O"   "O" "sp2" }
>> 	{ "O2"  "O" "sp2" }
>> 	{ "OP"  "O" "sp2" }
>> 	{ "OW"  "O" "sp3" }
>> 	{ "CT"  "C" "sp3" }
>> 	{ "CX"  "C" "sp3" }
>> 	{ "C8"  "C" "sp3" }
>> 	{ "2C"  "C" "sp3" }
>> 	{ "3C"  "C" "sp3" }
>> 	{ "CH"  "C" "sp3" }
>> 	{ "CS"  "C" "sp2" }
>> 	{ "C"   "C" "sp2" }
>> 	{ "CO"   "C" "sp2" }
>> 	{ "C*"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CB"  "C" "sp2" }
>> 	{ "CC"  "C" "sp2" }
>> 	{ "CN"  "C" "sp2" }
>> 	{ "CM"  "C" "sp2" }
>> 	{ "CK"  "C" "sp2" }
>> 	{ "CQ"  "C" "sp2" }
>> 	{ "CD"  "C" "sp2" }
>> 	{ "C5"  "C" "sp2" }
>> 	{ "C4"  "C" "sp2" }
>> 	{ "CP"  "C" "sp2" }
>> 	{ "CI"  "C" "sp3" }
>> 	{ "CJ"  "C" "sp2" }
>> 	{ "CW"  "C" "sp2" }
>> 	{ "CV"  "C" "sp2" }
>> 	{ "CR"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CY"  "C" "sp2" }
>> 	{ "C0"  "Ca" "sp3" }
>> 	{ "MG"  "Mg" "sp3" }
>> 	{ "N"   "N" "sp2" }
>> 	{ "NA"  "N" "sp2" }
>> 	{ "N2"  "N" "sp2" }
>> 	{ "N*"  "N" "sp2" }
>> 	{ "NP"  "N" "sp2" }
>> 	{ "NQ"  "N" "sp2" }
>> 	{ "NB"  "N" "sp2" }
>> 	{ "NC"  "N" "sp2" }
>> 	{ "NT"  "N" "sp3" }
>> 	{ "NY"  "N" "sp2" }
>> 	{ "N3"  "N" "sp3" }
>> 	{ "S"   "S" "sp3" }
>> 	{ "SH"  "S" "sp3" }
>> 	{ "P"   "P" "sp3" }
>> 	{ "LP"  ""  "sp3" }
>> 	{ "EP"  ""  "sp3" }
>> 	{ "F"   "F" "sp3" }
>> 	{ "Cl"  "Cl" "sp3" }
>> 	{ "Br"  "Br" "sp3" }
>> 	{ "I"   "I"  "sp3" }
>> 	{ "F-"   "F" "sp3" }
>> 	{ "Cl-"  "Cl" "sp3" }
>> 	{ "Br-"  "Br" "sp3" }
>> 	{ "I-"   "I"  "sp3" }
>> 	{ "Li+"  "Li"  "sp3" }
>> 	{ "Na+"  "Na"  "sp3" }
>> 	{ "K+"  "K"  "sp3" }
>> 	{ "Rb+"  "Rb"  "sp3" }
>> 	{ "Cs+"  "Cs"  "sp3" }
>> 	{ "Mg+"  "Mg"  "sp3" }
>> # glycam
>> 	{ "OG"  "O" "sp3" }
>> 	{ "OL"  "O" "sp3" }
>> 	{ "AC"  "C" "sp3" }
>> 	{ "EC"  "C" "sp3" }
>> }
>> #
>> #	Load the main parameter set.
>> #
>> parm10 = loadamberparams parm10.dat
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
(UNKNOWN ATOM TYPE: Zn)
(UNKNOWN ATOM TYPE: EP)
>> frcmod12SB = loadamberparams frcmod.ff12SB
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff12SB
Reading force field modification type file (frcmod)
Reading title:
ff12SB protein backbone and sidechain parameters
>> #
>> #	Load main chain and terminating amino acid libraries, nucleic acids
>> #
>> loadOff amino12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/amino12.lib
Loading: ALA
Loading: ARG
Loading: ASH
Loading: ASN
Loading: ASP
Loading: CYM
Loading: CYS
Loading: CYX
Loading: GLH
Loading: GLN
Loading: GLU
Loading: GLY
Loading: HID
Loading: HIE
Loading: HIP
Loading: HYP
Loading: ILE
Loading: LEU
Loading: LYN
Loading: LYS
Loading: MET
Loading: PHE
Loading: PRO
Loading: SER
Loading: THR
Loading: TRP
Loading: TYR
Loading: VAL
>> loadOff aminoct12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminoct12.lib
Loading: CALA
Loading: CARG
Loading: CASN
Loading: CASP
Loading: CCYS
Loading: CCYX
Loading: CGLN
Loading: CGLU
Loading: CGLY
Loading: CHID
Loading: CHIE
Loading: CHIP
Loading: CHYP
Loading: CILE
Loading: CLEU
Loading: CLYS
Loading: CMET
Loading: CPHE
Loading: CPRO
Loading: CSER
Loading: CTHR
Loading: CTRP
Loading: CTYR
Loading: CVAL
Loading: NHE
Loading: NME
>> loadOff aminont12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminont12.lib
Loading: ACE
Loading: NALA
Loading: NARG
Loading: NASN
Loading: NASP
Loading: NCYS
Loading: NCYX
Loading: NGLN
Loading: NGLU
Loading: NGLY
Loading: NHID
Loading: NHIE
Loading: NHIP
Loading: NILE
Loading: NLEU
Loading: NLYS
Loading: NMET
Loading: NPHE
Loading: NPRO
Loading: NSER
Loading: NTHR
Loading: NTRP
Loading: NTYR
Loading: NVAL
>> loadOff nucleic12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/nucleic12.lib
Loading: A
Loading: A3
Loading: A5
Loading: AN
Loading: C
Loading: C3
Loading: C5
Loading: CN
Loading: DA
Loading: DA3
Loading: DA5
Loading: DAN
Loading: DC
Loading: DC3
Loading: DC5
Loading: DCN
Loading: DG
Loading: DG3
Loading: DG5
Loading: DGN
Loading: DT
Loading: DT3
Loading: DT5
Loading: DTN
Loading: G
Loading: G3
Loading: G5
Loading: GN
Loading: OHE
Loading: U
Loading: U3
Loading: U5
Loading: UN
>> #
>> #       Load water and ions
>> # 
>> loadOff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
>> loadOff solvents.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: MEOHBOX
Loading: NMABOX
Loading: OPC
Loading: OPCBOX
Loading: PL3
Loading: POL3BOX
Loading: QSPCFWBOX
Loading: SPC
Loading: SPCBOX
Loading: SPCFWBOX
Loading: SPF
Loading: SPG
Loading: T4E
Loading: TIP3PBOX
Loading: TIP3PFBOX
Loading: TIP4PBOX
Loading: TIP4PEWBOX
Loading: TIP5PBOX
Loading: TP3
Loading: TP4
Loading: TP5
Loading: TPF
>> HOH = TP3
>> WAT = TP3
>> 
>> #
>> #	Define the PDB name map for the amino acids and nucleic acids
>> #     (note: no NHYP!  use neutral form for now)
>> #
>> addPdbResMap {
>>   { 0 "HYP" "HYP"  } { 1 "HYP" "CHYP" }
>>   { 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
>>   { 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
>>   { 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
>>   { 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
>>   { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
>>   { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
>>   { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
>>   { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
>>   { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
>>   { 0 "HID" "NHID" } { 1 "HID" "CHID" }
>>   { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
>>   { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
>>   { 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
>>   { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
>>   { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
>>   { 0 "MET" "NMET" } { 1 "MET" "CMET" }
>>   { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
>>   { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
>>   { 0 "SER" "NSER" } { 1 "SER" "CSER" }
>>   { 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
>>   { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
>>   { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
>>   { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
>>   { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
>>   { 0 "G" "G5"  } { 1 "G" "G3"  } 
>>   { 0 "A" "A5"  } { 1 "A" "A3"  } 
>>   { 0 "C" "C5"  } { 1 "C" "C3"  } 
>>   { 0 "U" "U5"  } { 1 "U" "U3"  } 
>>   { 0 "DG" "DG5"  } { 1 "DG" "DG3"  }  
>>   { 0 "DA" "DA5"  } { 1 "DA" "DA3"  }  
>>   { 0 "DC" "DC5"  } { 1 "DC" "DC3"  }  
>>   { 0 "DT" "DT5"  } { 1 "DT" "DT3"  }  
>> #  some old Amber residue names for RNA:
>>   { 0  "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" }
>>   { 0  "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" }
>>   { 0  "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" }
>>   { 0  "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" }
>> #  some really old Amber residue names, assuming DNA:
>>   { 0 "GUA" "DG5"  } { 1 "GUA" "DG3"  } { "GUA" "DG" }
>>   { 0 "ADE" "DA5"  } { 1 "ADE" "DA3"  } { "ADE" "DA" }
>>   { 0 "CYT" "DC5"  } { 1 "CYT" "DC3"  } { "CYT" "DC" }
>>   { 0 "THY" "DT5"  } { 1 "THY" "DT3"  } { "THY" "DT" }
>> #  uncomment out the following if you have this old style RNA files:
>> # { 0 "GUA" "G5"  } { 1 "GUA" "G3"  } { "GUA" "G" }
>> # { 0 "ADE" "A5"  } { 1 "ADE" "A3"  } { "ADE" "A" }
>> # { 0 "CYT" "C5"  } { 1 "CYT" "C3"  } { "CYT" "C" }
>> # { 0 "URA" "R5"  } { 1 "URA" "R3"  } { "URA" "R" }
>> 
>> }
>> 
>> #  try to be good about reading in really old atom names as well:
>> addPdbAtomMap {
>>   { "O5*" "O5'" }
>>   { "C5*" "C5'" }
>>   { "C4*" "C4'" }
>>   { "O4*" "O4'" }
>>   { "C3*" "C3'" }
>>   { "O3*" "O3'" }
>>   { "C2*" "C2'" }
>>   { "O2*" "O2'" }
>>   { "C1*" "C1'" }
>>   { "C5M" "C7"  }
>>   { "H1*" "H1'" }
>>   { "H2*1" "H2'" }
>>   { "H2*2" "H2''" }
>>   { "HO*2" "HO2'" }
>>   { "H2'1" "H2'" }
>>   { "H2'2" "H2''" }
>>   { "H3*" "H3'" }
>>   { "H4*" "H4'" }
>>   { "H5*1" "H5'" }
>>   { "H5*2" "H5''" }
>>   { "H5'1" "H5'" }
>>   { "H5'2" "H5''" }
>>   { "HO'2" "HO2'" }
>>   { "H5T"  "HO5'" }
>>   { "H3T"  "HO3'" }
>>   { "O1'" "O4'" }
>>   { "OA"  "OP1" }
>>   { "OB"  "OP2" }
>>   { "O1P" "OP1" }
>>   { "O2P" "OP2" }
>> }
>> 
>> #
>> # assume that most often proteins use HIE
>> #
>> NHIS = NHIE
>> HIS = HIE
>> CHIS = CHIE
> 
> loadoff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
> loadamberparams frcmod.opc
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.opc
Reading force field modification type file (frcmod)
Reading title:
Parameters for OPC water (JPCL, 2014, 5 (21), pp 3863–3871) 
(UNKNOWN ATOM TYPE: EP)
> loadamberparams frcmod.ionsjc_tip4pew
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip4pew
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP4P/EW water from Joung & Cheatham JPCB (2008)
> 
> m = loadpdb init.pdb
Loading PDB file: ./init.pdb
Enter zPdbReadScan from call depth  0.
Exit  zPdbReadScan from call depth  0.
Matching PDB residue names to LEaP variables.
(Residue 0: A5, Terminal/beginning, was not found in name map.)
(Residue 1: C3, Terminal/last, was not found in name map.)
Joining A5 - C3
  total atoms in file: 63
> 
> 
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.131155 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<H4' 9>
Warning: Close contact of 1.307451 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<C4' 8>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> solvatebox m OPCBOX 10.66 iso
  Solute vdw bounding box:              12.265 11.150 10.292
  Total bounding box for atom centers:  33.585 33.585 33.585
      (box expansion for 'iso' is   9.9%)
  Solvent unit box:                     18.865 18.478 19.006
The number of boxes:  x= 2  y= 2  z= 2
Adding box at: x=0  y=0  z=0
Center of solvent box is: 9.432422, 9.239054, 9.503120
Adding box at: x=0  y=0  z=1
Center of solvent box is: 9.432422, 9.239054, -9.503120
Adding box at: x=0  y=1  z=0
Center of solvent box is: 9.432422, -9.239054, 9.503120
Adding box at: x=0  y=1  z=1
Center of solvent box is: 9.432422, -9.239054, -9.503120
Adding box at: x=1  y=0  z=0
Center of solvent box is: -9.432422, 9.239054, 9.503120
Adding box at: x=1  y=0  z=1
Center of solvent box is: -9.432422, 9.239054, -9.503120
Adding box at: x=1  y=1  z=0
Center of solvent box is: -9.432422, -9.239054, 9.503120
Adding box at: x=1  y=1  z=1
Center of solvent box is: -9.432422, -9.239054, -9.503120
  Volume: 48622.506 A^3 
  Total mass 20100.776 amu,  Density 0.686 g/cc
  Added 1084 residues.
> quit
	Quit
log started: Sun Nov  1 20:53:04 2015

Log file: ./leap.log
>> #
>> # ----- leaprc for loading the ff12SB force field
>> # ----- NOTE: this is designed for PDB format 3!
>> #    Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA
>> #
>> #	load atom type hybridizations
>> #
>> addAtomTypes {
>> 	{ "H"   "H" "sp3" }
>> 	{ "HO"  "H" "sp3" }
>> 	{ "HS"  "H" "sp3" }
>> 	{ "H1"  "H" "sp3" }
>> 	{ "H2"  "H" "sp3" }
>> 	{ "H3"  "H" "sp3" }
>> 	{ "H4"  "H" "sp3" }
>> 	{ "H5"  "H" "sp3" }
>> 	{ "HW"  "H" "sp3" }
>> 	{ "HC"  "H" "sp3" }
>> 	{ "HA"  "H" "sp3" }
>> 	{ "HP"  "H" "sp3" }
>> 	{ "HZ"  "H" "sp3" }
>> 	{ "OH"  "O" "sp3" }
>> 	{ "OS"  "O" "sp3" }
>> 	{ "O"   "O" "sp2" }
>> 	{ "O2"  "O" "sp2" }
>> 	{ "OP"  "O" "sp2" }
>> 	{ "OW"  "O" "sp3" }
>> 	{ "CT"  "C" "sp3" }
>> 	{ "CX"  "C" "sp3" }
>> 	{ "C8"  "C" "sp3" }
>> 	{ "2C"  "C" "sp3" }
>> 	{ "3C"  "C" "sp3" }
>> 	{ "CH"  "C" "sp3" }
>> 	{ "CS"  "C" "sp2" }
>> 	{ "C"   "C" "sp2" }
>> 	{ "CO"   "C" "sp2" }
>> 	{ "C*"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CB"  "C" "sp2" }
>> 	{ "CC"  "C" "sp2" }
>> 	{ "CN"  "C" "sp2" }
>> 	{ "CM"  "C" "sp2" }
>> 	{ "CK"  "C" "sp2" }
>> 	{ "CQ"  "C" "sp2" }
>> 	{ "CD"  "C" "sp2" }
>> 	{ "C5"  "C" "sp2" }
>> 	{ "C4"  "C" "sp2" }
>> 	{ "CP"  "C" "sp2" }
>> 	{ "CI"  "C" "sp3" }
>> 	{ "CJ"  "C" "sp2" }
>> 	{ "CW"  "C" "sp2" }
>> 	{ "CV"  "C" "sp2" }
>> 	{ "CR"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CY"  "C" "sp2" }
>> 	{ "C0"  "Ca" "sp3" }
>> 	{ "MG"  "Mg" "sp3" }
>> 	{ "N"   "N" "sp2" }
>> 	{ "NA"  "N" "sp2" }
>> 	{ "N2"  "N" "sp2" }
>> 	{ "N*"  "N" "sp2" }
>> 	{ "NP"  "N" "sp2" }
>> 	{ "NQ"  "N" "sp2" }
>> 	{ "NB"  "N" "sp2" }
>> 	{ "NC"  "N" "sp2" }
>> 	{ "NT"  "N" "sp3" }
>> 	{ "NY"  "N" "sp2" }
>> 	{ "N3"  "N" "sp3" }
>> 	{ "S"   "S" "sp3" }
>> 	{ "SH"  "S" "sp3" }
>> 	{ "P"   "P" "sp3" }
>> 	{ "LP"  ""  "sp3" }
>> 	{ "EP"  ""  "sp3" }
>> 	{ "F"   "F" "sp3" }
>> 	{ "Cl"  "Cl" "sp3" }
>> 	{ "Br"  "Br" "sp3" }
>> 	{ "I"   "I"  "sp3" }
>> 	{ "F-"   "F" "sp3" }
>> 	{ "Cl-"  "Cl" "sp3" }
>> 	{ "Br-"  "Br" "sp3" }
>> 	{ "I-"   "I"  "sp3" }
>> 	{ "Li+"  "Li"  "sp3" }
>> 	{ "Na+"  "Na"  "sp3" }
>> 	{ "K+"  "K"  "sp3" }
>> 	{ "Rb+"  "Rb"  "sp3" }
>> 	{ "Cs+"  "Cs"  "sp3" }
>> 	{ "Mg+"  "Mg"  "sp3" }
>> # glycam
>> 	{ "OG"  "O" "sp3" }
>> 	{ "OL"  "O" "sp3" }
>> 	{ "AC"  "C" "sp3" }
>> 	{ "EC"  "C" "sp3" }
>> }
>> #
>> #	Load the main parameter set.
>> #
>> parm10 = loadamberparams parm10.dat
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
(UNKNOWN ATOM TYPE: Zn)
(UNKNOWN ATOM TYPE: EP)
>> frcmod12SB = loadamberparams frcmod.ff12SB
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff12SB
Reading force field modification type file (frcmod)
Reading title:
ff12SB protein backbone and sidechain parameters
>> #
>> #	Load main chain and terminating amino acid libraries, nucleic acids
>> #
>> loadOff amino12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/amino12.lib
Loading: ALA
Loading: ARG
Loading: ASH
Loading: ASN
Loading: ASP
Loading: CYM
Loading: CYS
Loading: CYX
Loading: GLH
Loading: GLN
Loading: GLU
Loading: GLY
Loading: HID
Loading: HIE
Loading: HIP
Loading: HYP
Loading: ILE
Loading: LEU
Loading: LYN
Loading: LYS
Loading: MET
Loading: PHE
Loading: PRO
Loading: SER
Loading: THR
Loading: TRP
Loading: TYR
Loading: VAL
>> loadOff aminoct12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminoct12.lib
Loading: CALA
Loading: CARG
Loading: CASN
Loading: CASP
Loading: CCYS
Loading: CCYX
Loading: CGLN
Loading: CGLU
Loading: CGLY
Loading: CHID
Loading: CHIE
Loading: CHIP
Loading: CHYP
Loading: CILE
Loading: CLEU
Loading: CLYS
Loading: CMET
Loading: CPHE
Loading: CPRO
Loading: CSER
Loading: CTHR
Loading: CTRP
Loading: CTYR
Loading: CVAL
Loading: NHE
Loading: NME
>> loadOff aminont12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminont12.lib
Loading: ACE
Loading: NALA
Loading: NARG
Loading: NASN
Loading: NASP
Loading: NCYS
Loading: NCYX
Loading: NGLN
Loading: NGLU
Loading: NGLY
Loading: NHID
Loading: NHIE
Loading: NHIP
Loading: NILE
Loading: NLEU
Loading: NLYS
Loading: NMET
Loading: NPHE
Loading: NPRO
Loading: NSER
Loading: NTHR
Loading: NTRP
Loading: NTYR
Loading: NVAL
>> loadOff nucleic12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/nucleic12.lib
Loading: A
Loading: A3
Loading: A5
Loading: AN
Loading: C
Loading: C3
Loading: C5
Loading: CN
Loading: DA
Loading: DA3
Loading: DA5
Loading: DAN
Loading: DC
Loading: DC3
Loading: DC5
Loading: DCN
Loading: DG
Loading: DG3
Loading: DG5
Loading: DGN
Loading: DT
Loading: DT3
Loading: DT5
Loading: DTN
Loading: G
Loading: G3
Loading: G5
Loading: GN
Loading: OHE
Loading: U
Loading: U3
Loading: U5
Loading: UN
>> #
>> #       Load water and ions
>> # 
>> loadOff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
>> loadOff solvents.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: MEOHBOX
Loading: NMABOX
Loading: OPC
Loading: OPCBOX
Loading: PL3
Loading: POL3BOX
Loading: QSPCFWBOX
Loading: SPC
Loading: SPCBOX
Loading: SPCFWBOX
Loading: SPF
Loading: SPG
Loading: T4E
Loading: TIP3PBOX
Loading: TIP3PFBOX
Loading: TIP4PBOX
Loading: TIP4PEWBOX
Loading: TIP5PBOX
Loading: TP3
Loading: TP4
Loading: TP5
Loading: TPF
>> HOH = TP3
>> WAT = TP3
>> 
>> #
>> #	Define the PDB name map for the amino acids and nucleic acids
>> #     (note: no NHYP!  use neutral form for now)
>> #
>> addPdbResMap {
>>   { 0 "HYP" "HYP"  } { 1 "HYP" "CHYP" }
>>   { 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
>>   { 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
>>   { 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
>>   { 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
>>   { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
>>   { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
>>   { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
>>   { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
>>   { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
>>   { 0 "HID" "NHID" } { 1 "HID" "CHID" }
>>   { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
>>   { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
>>   { 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
>>   { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
>>   { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
>>   { 0 "MET" "NMET" } { 1 "MET" "CMET" }
>>   { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
>>   { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
>>   { 0 "SER" "NSER" } { 1 "SER" "CSER" }
>>   { 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
>>   { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
>>   { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
>>   { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
>>   { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
>>   { 0 "G" "G5"  } { 1 "G" "G3"  } 
>>   { 0 "A" "A5"  } { 1 "A" "A3"  } 
>>   { 0 "C" "C5"  } { 1 "C" "C3"  } 
>>   { 0 "U" "U5"  } { 1 "U" "U3"  } 
>>   { 0 "DG" "DG5"  } { 1 "DG" "DG3"  }  
>>   { 0 "DA" "DA5"  } { 1 "DA" "DA3"  }  
>>   { 0 "DC" "DC5"  } { 1 "DC" "DC3"  }  
>>   { 0 "DT" "DT5"  } { 1 "DT" "DT3"  }  
>> #  some old Amber residue names for RNA:
>>   { 0  "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" }
>>   { 0  "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" }
>>   { 0  "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" }
>>   { 0  "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" }
>> #  some really old Amber residue names, assuming DNA:
>>   { 0 "GUA" "DG5"  } { 1 "GUA" "DG3"  } { "GUA" "DG" }
>>   { 0 "ADE" "DA5"  } { 1 "ADE" "DA3"  } { "ADE" "DA" }
>>   { 0 "CYT" "DC5"  } { 1 "CYT" "DC3"  } { "CYT" "DC" }
>>   { 0 "THY" "DT5"  } { 1 "THY" "DT3"  } { "THY" "DT" }
>> #  uncomment out the following if you have this old style RNA files:
>> # { 0 "GUA" "G5"  } { 1 "GUA" "G3"  } { "GUA" "G" }
>> # { 0 "ADE" "A5"  } { 1 "ADE" "A3"  } { "ADE" "A" }
>> # { 0 "CYT" "C5"  } { 1 "CYT" "C3"  } { "CYT" "C" }
>> # { 0 "URA" "R5"  } { 1 "URA" "R3"  } { "URA" "R" }
>> 
>> }
>> 
>> #  try to be good about reading in really old atom names as well:
>> addPdbAtomMap {
>>   { "O5*" "O5'" }
>>   { "C5*" "C5'" }
>>   { "C4*" "C4'" }
>>   { "O4*" "O4'" }
>>   { "C3*" "C3'" }
>>   { "O3*" "O3'" }
>>   { "C2*" "C2'" }
>>   { "O2*" "O2'" }
>>   { "C1*" "C1'" }
>>   { "C5M" "C7"  }
>>   { "H1*" "H1'" }
>>   { "H2*1" "H2'" }
>>   { "H2*2" "H2''" }
>>   { "HO*2" "HO2'" }
>>   { "H2'1" "H2'" }
>>   { "H2'2" "H2''" }
>>   { "H3*" "H3'" }
>>   { "H4*" "H4'" }
>>   { "H5*1" "H5'" }
>>   { "H5*2" "H5''" }
>>   { "H5'1" "H5'" }
>>   { "H5'2" "H5''" }
>>   { "HO'2" "HO2'" }
>>   { "H5T"  "HO5'" }
>>   { "H3T"  "HO3'" }
>>   { "O1'" "O4'" }
>>   { "OA"  "OP1" }
>>   { "OB"  "OP2" }
>>   { "O1P" "OP1" }
>>   { "O2P" "OP2" }
>> }
>> 
>> #
>> # assume that most often proteins use HIE
>> #
>> NHIS = NHIE
>> HIS = HIE
>> CHIS = CHIE
> 
> loadoff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
> loadamberparams frcmod.opc
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.opc
Reading force field modification type file (frcmod)
Reading title:
Parameters for OPC water (JPCL, 2014, 5 (21), pp 3863–3871) 
(UNKNOWN ATOM TYPE: EP)
> loadamberparams frcmod.ionsjc_tip4pew
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip4pew
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP4P/EW water from Joung & Cheatham JPCB (2008)
> 
> m = loadpdb init.pdb
Loading PDB file: ./init.pdb
Enter zPdbReadScan from call depth  0.
Exit  zPdbReadScan from call depth  0.
Matching PDB residue names to LEaP variables.
(Residue 0: A5, Terminal/beginning, was not found in name map.)
(Residue 1: C3, Terminal/last, was not found in name map.)
Joining A5 - C3
  total atoms in file: 63
> 
> 
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.131155 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<H4' 9>
Warning: Close contact of 1.307451 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<C4' 8>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> solvatebox m OPCBOX 10.67 iso
  Solute vdw bounding box:              12.265 11.150 10.292
  Total bounding box for atom centers:  33.605 33.605 33.605
      (box expansion for 'iso' is   9.9%)
  Solvent unit box:                     18.865 18.478 19.006
The number of boxes:  x= 2  y= 2  z= 2
Adding box at: x=0  y=0  z=0
Center of solvent box is: 9.432422, 9.239054, 9.503120
Adding box at: x=0  y=0  z=1
Center of solvent box is: 9.432422, 9.239054, -9.503120
Adding box at: x=0  y=1  z=0
Center of solvent box is: 9.432422, -9.239054, 9.503120
Adding box at: x=0  y=1  z=1
Center of solvent box is: 9.432422, -9.239054, -9.503120
Adding box at: x=1  y=0  z=0
Center of solvent box is: -9.432422, 9.239054, 9.503120
Adding box at: x=1  y=0  z=1
Center of solvent box is: -9.432422, 9.239054, -9.503120
Adding box at: x=1  y=1  z=0
Center of solvent box is: -9.432422, -9.239054, 9.503120
Adding box at: x=1  y=1  z=1
Center of solvent box is: -9.432422, -9.239054, -9.503120
  Volume: 48622.506 A^3 
  Total mass 20100.776 amu,  Density 0.686 g/cc
  Added 1084 residues.
> quit
	Quit
log started: Sun Nov  1 20:53:04 2015

Log file: ./leap.log
>> #
>> # ----- leaprc for loading the ff12SB force field
>> # ----- NOTE: this is designed for PDB format 3!
>> #    Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA
>> #
>> #	load atom type hybridizations
>> #
>> addAtomTypes {
>> 	{ "H"   "H" "sp3" }
>> 	{ "HO"  "H" "sp3" }
>> 	{ "HS"  "H" "sp3" }
>> 	{ "H1"  "H" "sp3" }
>> 	{ "H2"  "H" "sp3" }
>> 	{ "H3"  "H" "sp3" }
>> 	{ "H4"  "H" "sp3" }
>> 	{ "H5"  "H" "sp3" }
>> 	{ "HW"  "H" "sp3" }
>> 	{ "HC"  "H" "sp3" }
>> 	{ "HA"  "H" "sp3" }
>> 	{ "HP"  "H" "sp3" }
>> 	{ "HZ"  "H" "sp3" }
>> 	{ "OH"  "O" "sp3" }
>> 	{ "OS"  "O" "sp3" }
>> 	{ "O"   "O" "sp2" }
>> 	{ "O2"  "O" "sp2" }
>> 	{ "OP"  "O" "sp2" }
>> 	{ "OW"  "O" "sp3" }
>> 	{ "CT"  "C" "sp3" }
>> 	{ "CX"  "C" "sp3" }
>> 	{ "C8"  "C" "sp3" }
>> 	{ "2C"  "C" "sp3" }
>> 	{ "3C"  "C" "sp3" }
>> 	{ "CH"  "C" "sp3" }
>> 	{ "CS"  "C" "sp2" }
>> 	{ "C"   "C" "sp2" }
>> 	{ "CO"   "C" "sp2" }
>> 	{ "C*"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CB"  "C" "sp2" }
>> 	{ "CC"  "C" "sp2" }
>> 	{ "CN"  "C" "sp2" }
>> 	{ "CM"  "C" "sp2" }
>> 	{ "CK"  "C" "sp2" }
>> 	{ "CQ"  "C" "sp2" }
>> 	{ "CD"  "C" "sp2" }
>> 	{ "C5"  "C" "sp2" }
>> 	{ "C4"  "C" "sp2" }
>> 	{ "CP"  "C" "sp2" }
>> 	{ "CI"  "C" "sp3" }
>> 	{ "CJ"  "C" "sp2" }
>> 	{ "CW"  "C" "sp2" }
>> 	{ "CV"  "C" "sp2" }
>> 	{ "CR"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CY"  "C" "sp2" }
>> 	{ "C0"  "Ca" "sp3" }
>> 	{ "MG"  "Mg" "sp3" }
>> 	{ "N"   "N" "sp2" }
>> 	{ "NA"  "N" "sp2" }
>> 	{ "N2"  "N" "sp2" }
>> 	{ "N*"  "N" "sp2" }
>> 	{ "NP"  "N" "sp2" }
>> 	{ "NQ"  "N" "sp2" }
>> 	{ "NB"  "N" "sp2" }
>> 	{ "NC"  "N" "sp2" }
>> 	{ "NT"  "N" "sp3" }
>> 	{ "NY"  "N" "sp2" }
>> 	{ "N3"  "N" "sp3" }
>> 	{ "S"   "S" "sp3" }
>> 	{ "SH"  "S" "sp3" }
>> 	{ "P"   "P" "sp3" }
>> 	{ "LP"  ""  "sp3" }
>> 	{ "EP"  ""  "sp3" }
>> 	{ "F"   "F" "sp3" }
>> 	{ "Cl"  "Cl" "sp3" }
>> 	{ "Br"  "Br" "sp3" }
>> 	{ "I"   "I"  "sp3" }
>> 	{ "F-"   "F" "sp3" }
>> 	{ "Cl-"  "Cl" "sp3" }
>> 	{ "Br-"  "Br" "sp3" }
>> 	{ "I-"   "I"  "sp3" }
>> 	{ "Li+"  "Li"  "sp3" }
>> 	{ "Na+"  "Na"  "sp3" }
>> 	{ "K+"  "K"  "sp3" }
>> 	{ "Rb+"  "Rb"  "sp3" }
>> 	{ "Cs+"  "Cs"  "sp3" }
>> 	{ "Mg+"  "Mg"  "sp3" }
>> # glycam
>> 	{ "OG"  "O" "sp3" }
>> 	{ "OL"  "O" "sp3" }
>> 	{ "AC"  "C" "sp3" }
>> 	{ "EC"  "C" "sp3" }
>> }
>> #
>> #	Load the main parameter set.
>> #
>> parm10 = loadamberparams parm10.dat
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
(UNKNOWN ATOM TYPE: Zn)
(UNKNOWN ATOM TYPE: EP)
>> frcmod12SB = loadamberparams frcmod.ff12SB
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff12SB
Reading force field modification type file (frcmod)
Reading title:
ff12SB protein backbone and sidechain parameters
>> #
>> #	Load main chain and terminating amino acid libraries, nucleic acids
>> #
>> loadOff amino12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/amino12.lib
Loading: ALA
Loading: ARG
Loading: ASH
Loading: ASN
Loading: ASP
Loading: CYM
Loading: CYS
Loading: CYX
Loading: GLH
Loading: GLN
Loading: GLU
Loading: GLY
Loading: HID
Loading: HIE
Loading: HIP
Loading: HYP
Loading: ILE
Loading: LEU
Loading: LYN
Loading: LYS
Loading: MET
Loading: PHE
Loading: PRO
Loading: SER
Loading: THR
Loading: TRP
Loading: TYR
Loading: VAL
>> loadOff aminoct12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminoct12.lib
Loading: CALA
Loading: CARG
Loading: CASN
Loading: CASP
Loading: CCYS
Loading: CCYX
Loading: CGLN
Loading: CGLU
Loading: CGLY
Loading: CHID
Loading: CHIE
Loading: CHIP
Loading: CHYP
Loading: CILE
Loading: CLEU
Loading: CLYS
Loading: CMET
Loading: CPHE
Loading: CPRO
Loading: CSER
Loading: CTHR
Loading: CTRP
Loading: CTYR
Loading: CVAL
Loading: NHE
Loading: NME
>> loadOff aminont12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminont12.lib
Loading: ACE
Loading: NALA
Loading: NARG
Loading: NASN
Loading: NASP
Loading: NCYS
Loading: NCYX
Loading: NGLN
Loading: NGLU
Loading: NGLY
Loading: NHID
Loading: NHIE
Loading: NHIP
Loading: NILE
Loading: NLEU
Loading: NLYS
Loading: NMET
Loading: NPHE
Loading: NPRO
Loading: NSER
Loading: NTHR
Loading: NTRP
Loading: NTYR
Loading: NVAL
>> loadOff nucleic12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/nucleic12.lib
Loading: A
Loading: A3
Loading: A5
Loading: AN
Loading: C
Loading: C3
Loading: C5
Loading: CN
Loading: DA
Loading: DA3
Loading: DA5
Loading: DAN
Loading: DC
Loading: DC3
Loading: DC5
Loading: DCN
Loading: DG
Loading: DG3
Loading: DG5
Loading: DGN
Loading: DT
Loading: DT3
Loading: DT5
Loading: DTN
Loading: G
Loading: G3
Loading: G5
Loading: GN
Loading: OHE
Loading: U
Loading: U3
Loading: U5
Loading: UN
>> #
>> #       Load water and ions
>> # 
>> loadOff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
>> loadOff solvents.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: MEOHBOX
Loading: NMABOX
Loading: OPC
Loading: OPCBOX
Loading: PL3
Loading: POL3BOX
Loading: QSPCFWBOX
Loading: SPC
Loading: SPCBOX
Loading: SPCFWBOX
Loading: SPF
Loading: SPG
Loading: T4E
Loading: TIP3PBOX
Loading: TIP3PFBOX
Loading: TIP4PBOX
Loading: TIP4PEWBOX
Loading: TIP5PBOX
Loading: TP3
Loading: TP4
Loading: TP5
Loading: TPF
>> HOH = TP3
>> WAT = TP3
>> 
>> #
>> #	Define the PDB name map for the amino acids and nucleic acids
>> #     (note: no NHYP!  use neutral form for now)
>> #
>> addPdbResMap {
>>   { 0 "HYP" "HYP"  } { 1 "HYP" "CHYP" }
>>   { 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
>>   { 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
>>   { 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
>>   { 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
>>   { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
>>   { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
>>   { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
>>   { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
>>   { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
>>   { 0 "HID" "NHID" } { 1 "HID" "CHID" }
>>   { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
>>   { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
>>   { 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
>>   { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
>>   { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
>>   { 0 "MET" "NMET" } { 1 "MET" "CMET" }
>>   { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
>>   { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
>>   { 0 "SER" "NSER" } { 1 "SER" "CSER" }
>>   { 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
>>   { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
>>   { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
>>   { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
>>   { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
>>   { 0 "G" "G5"  } { 1 "G" "G3"  } 
>>   { 0 "A" "A5"  } { 1 "A" "A3"  } 
>>   { 0 "C" "C5"  } { 1 "C" "C3"  } 
>>   { 0 "U" "U5"  } { 1 "U" "U3"  } 
>>   { 0 "DG" "DG5"  } { 1 "DG" "DG3"  }  
>>   { 0 "DA" "DA5"  } { 1 "DA" "DA3"  }  
>>   { 0 "DC" "DC5"  } { 1 "DC" "DC3"  }  
>>   { 0 "DT" "DT5"  } { 1 "DT" "DT3"  }  
>> #  some old Amber residue names for RNA:
>>   { 0  "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" }
>>   { 0  "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" }
>>   { 0  "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" }
>>   { 0  "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" }
>> #  some really old Amber residue names, assuming DNA:
>>   { 0 "GUA" "DG5"  } { 1 "GUA" "DG3"  } { "GUA" "DG" }
>>   { 0 "ADE" "DA5"  } { 1 "ADE" "DA3"  } { "ADE" "DA" }
>>   { 0 "CYT" "DC5"  } { 1 "CYT" "DC3"  } { "CYT" "DC" }
>>   { 0 "THY" "DT5"  } { 1 "THY" "DT3"  } { "THY" "DT" }
>> #  uncomment out the following if you have this old style RNA files:
>> # { 0 "GUA" "G5"  } { 1 "GUA" "G3"  } { "GUA" "G" }
>> # { 0 "ADE" "A5"  } { 1 "ADE" "A3"  } { "ADE" "A" }
>> # { 0 "CYT" "C5"  } { 1 "CYT" "C3"  } { "CYT" "C" }
>> # { 0 "URA" "R5"  } { 1 "URA" "R3"  } { "URA" "R" }
>> 
>> }
>> 
>> #  try to be good about reading in really old atom names as well:
>> addPdbAtomMap {
>>   { "O5*" "O5'" }
>>   { "C5*" "C5'" }
>>   { "C4*" "C4'" }
>>   { "O4*" "O4'" }
>>   { "C3*" "C3'" }
>>   { "O3*" "O3'" }
>>   { "C2*" "C2'" }
>>   { "O2*" "O2'" }
>>   { "C1*" "C1'" }
>>   { "C5M" "C7"  }
>>   { "H1*" "H1'" }
>>   { "H2*1" "H2'" }
>>   { "H2*2" "H2''" }
>>   { "HO*2" "HO2'" }
>>   { "H2'1" "H2'" }
>>   { "H2'2" "H2''" }
>>   { "H3*" "H3'" }
>>   { "H4*" "H4'" }
>>   { "H5*1" "H5'" }
>>   { "H5*2" "H5''" }
>>   { "H5'1" "H5'" }
>>   { "H5'2" "H5''" }
>>   { "HO'2" "HO2'" }
>>   { "H5T"  "HO5'" }
>>   { "H3T"  "HO3'" }
>>   { "O1'" "O4'" }
>>   { "OA"  "OP1" }
>>   { "OB"  "OP2" }
>>   { "O1P" "OP1" }
>>   { "O2P" "OP2" }
>> }
>> 
>> #
>> # assume that most often proteins use HIE
>> #
>> NHIS = NHIE
>> HIS = HIE
>> CHIS = CHIE
> 
> loadoff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
> loadamberparams frcmod.opc
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.opc
Reading force field modification type file (frcmod)
Reading title:
Parameters for OPC water (JPCL, 2014, 5 (21), pp 3863–3871) 
(UNKNOWN ATOM TYPE: EP)
> loadamberparams frcmod.ionsjc_tip4pew
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip4pew
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP4P/EW water from Joung & Cheatham JPCB (2008)
> 
> m = loadpdb init.pdb
Loading PDB file: ./init.pdb
Enter zPdbReadScan from call depth  0.
Exit  zPdbReadScan from call depth  0.
Matching PDB residue names to LEaP variables.
(Residue 0: A5, Terminal/beginning, was not found in name map.)
(Residue 1: C3, Terminal/last, was not found in name map.)
Joining A5 - C3
  total atoms in file: 63
> 
> 
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.131155 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<H4' 9>
Warning: Close contact of 1.307451 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<C4' 8>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> solvatebox m OPCBOX 10.68 iso
  Solute vdw bounding box:              12.265 11.150 10.292
  Total bounding box for atom centers:  33.625 33.625 33.625
      (box expansion for 'iso' is   9.9%)
  Solvent unit box:                     18.865 18.478 19.006
The number of boxes:  x= 2  y= 2  z= 2
Adding box at: x=0  y=0  z=0
Center of solvent box is: 9.432422, 9.239054, 9.503120
Adding box at: x=0  y=0  z=1
Center of solvent box is: 9.432422, 9.239054, -9.503120
Adding box at: x=0  y=1  z=0
Center of solvent box is: 9.432422, -9.239054, 9.503120
Adding box at: x=0  y=1  z=1
Center of solvent box is: 9.432422, -9.239054, -9.503120
Adding box at: x=1  y=0  z=0
Center of solvent box is: -9.432422, 9.239054, 9.503120
Adding box at: x=1  y=0  z=1
Center of solvent box is: -9.432422, 9.239054, -9.503120
Adding box at: x=1  y=1  z=0
Center of solvent box is: -9.432422, -9.239054, 9.503120
Adding box at: x=1  y=1  z=1
Center of solvent box is: -9.432422, -9.239054, -9.503120
  Volume: 48622.506 A^3 
  Total mass 20100.776 amu,  Density 0.686 g/cc
  Added 1084 residues.
> quit
	Quit
log started: Sun Nov  1 20:53:04 2015

Log file: ./leap.log
>> #
>> # ----- leaprc for loading the ff12SB force field
>> # ----- NOTE: this is designed for PDB format 3!
>> #    Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA
>> #
>> #	load atom type hybridizations
>> #
>> addAtomTypes {
>> 	{ "H"   "H" "sp3" }
>> 	{ "HO"  "H" "sp3" }
>> 	{ "HS"  "H" "sp3" }
>> 	{ "H1"  "H" "sp3" }
>> 	{ "H2"  "H" "sp3" }
>> 	{ "H3"  "H" "sp3" }
>> 	{ "H4"  "H" "sp3" }
>> 	{ "H5"  "H" "sp3" }
>> 	{ "HW"  "H" "sp3" }
>> 	{ "HC"  "H" "sp3" }
>> 	{ "HA"  "H" "sp3" }
>> 	{ "HP"  "H" "sp3" }
>> 	{ "HZ"  "H" "sp3" }
>> 	{ "OH"  "O" "sp3" }
>> 	{ "OS"  "O" "sp3" }
>> 	{ "O"   "O" "sp2" }
>> 	{ "O2"  "O" "sp2" }
>> 	{ "OP"  "O" "sp2" }
>> 	{ "OW"  "O" "sp3" }
>> 	{ "CT"  "C" "sp3" }
>> 	{ "CX"  "C" "sp3" }
>> 	{ "C8"  "C" "sp3" }
>> 	{ "2C"  "C" "sp3" }
>> 	{ "3C"  "C" "sp3" }
>> 	{ "CH"  "C" "sp3" }
>> 	{ "CS"  "C" "sp2" }
>> 	{ "C"   "C" "sp2" }
>> 	{ "CO"   "C" "sp2" }
>> 	{ "C*"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CB"  "C" "sp2" }
>> 	{ "CC"  "C" "sp2" }
>> 	{ "CN"  "C" "sp2" }
>> 	{ "CM"  "C" "sp2" }
>> 	{ "CK"  "C" "sp2" }
>> 	{ "CQ"  "C" "sp2" }
>> 	{ "CD"  "C" "sp2" }
>> 	{ "C5"  "C" "sp2" }
>> 	{ "C4"  "C" "sp2" }
>> 	{ "CP"  "C" "sp2" }
>> 	{ "CI"  "C" "sp3" }
>> 	{ "CJ"  "C" "sp2" }
>> 	{ "CW"  "C" "sp2" }
>> 	{ "CV"  "C" "sp2" }
>> 	{ "CR"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CY"  "C" "sp2" }
>> 	{ "C0"  "Ca" "sp3" }
>> 	{ "MG"  "Mg" "sp3" }
>> 	{ "N"   "N" "sp2" }
>> 	{ "NA"  "N" "sp2" }
>> 	{ "N2"  "N" "sp2" }
>> 	{ "N*"  "N" "sp2" }
>> 	{ "NP"  "N" "sp2" }
>> 	{ "NQ"  "N" "sp2" }
>> 	{ "NB"  "N" "sp2" }
>> 	{ "NC"  "N" "sp2" }
>> 	{ "NT"  "N" "sp3" }
>> 	{ "NY"  "N" "sp2" }
>> 	{ "N3"  "N" "sp3" }
>> 	{ "S"   "S" "sp3" }
>> 	{ "SH"  "S" "sp3" }
>> 	{ "P"   "P" "sp3" }
>> 	{ "LP"  ""  "sp3" }
>> 	{ "EP"  ""  "sp3" }
>> 	{ "F"   "F" "sp3" }
>> 	{ "Cl"  "Cl" "sp3" }
>> 	{ "Br"  "Br" "sp3" }
>> 	{ "I"   "I"  "sp3" }
>> 	{ "F-"   "F" "sp3" }
>> 	{ "Cl-"  "Cl" "sp3" }
>> 	{ "Br-"  "Br" "sp3" }
>> 	{ "I-"   "I"  "sp3" }
>> 	{ "Li+"  "Li"  "sp3" }
>> 	{ "Na+"  "Na"  "sp3" }
>> 	{ "K+"  "K"  "sp3" }
>> 	{ "Rb+"  "Rb"  "sp3" }
>> 	{ "Cs+"  "Cs"  "sp3" }
>> 	{ "Mg+"  "Mg"  "sp3" }
>> # glycam
>> 	{ "OG"  "O" "sp3" }
>> 	{ "OL"  "O" "sp3" }
>> 	{ "AC"  "C" "sp3" }
>> 	{ "EC"  "C" "sp3" }
>> }
>> #
>> #	Load the main parameter set.
>> #
>> parm10 = loadamberparams parm10.dat
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
(UNKNOWN ATOM TYPE: Zn)
(UNKNOWN ATOM TYPE: EP)
>> frcmod12SB = loadamberparams frcmod.ff12SB
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff12SB
Reading force field modification type file (frcmod)
Reading title:
ff12SB protein backbone and sidechain parameters
>> #
>> #	Load main chain and terminating amino acid libraries, nucleic acids
>> #
>> loadOff amino12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/amino12.lib
Loading: ALA
Loading: ARG
Loading: ASH
Loading: ASN
Loading: ASP
Loading: CYM
Loading: CYS
Loading: CYX
Loading: GLH
Loading: GLN
Loading: GLU
Loading: GLY
Loading: HID
Loading: HIE
Loading: HIP
Loading: HYP
Loading: ILE
Loading: LEU
Loading: LYN
Loading: LYS
Loading: MET
Loading: PHE
Loading: PRO
Loading: SER
Loading: THR
Loading: TRP
Loading: TYR
Loading: VAL
>> loadOff aminoct12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminoct12.lib
Loading: CALA
Loading: CARG
Loading: CASN
Loading: CASP
Loading: CCYS
Loading: CCYX
Loading: CGLN
Loading: CGLU
Loading: CGLY
Loading: CHID
Loading: CHIE
Loading: CHIP
Loading: CHYP
Loading: CILE
Loading: CLEU
Loading: CLYS
Loading: CMET
Loading: CPHE
Loading: CPRO
Loading: CSER
Loading: CTHR
Loading: CTRP
Loading: CTYR
Loading: CVAL
Loading: NHE
Loading: NME
>> loadOff aminont12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminont12.lib
Loading: ACE
Loading: NALA
Loading: NARG
Loading: NASN
Loading: NASP
Loading: NCYS
Loading: NCYX
Loading: NGLN
Loading: NGLU
Loading: NGLY
Loading: NHID
Loading: NHIE
Loading: NHIP
Loading: NILE
Loading: NLEU
Loading: NLYS
Loading: NMET
Loading: NPHE
Loading: NPRO
Loading: NSER
Loading: NTHR
Loading: NTRP
Loading: NTYR
Loading: NVAL
>> loadOff nucleic12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/nucleic12.lib
Loading: A
Loading: A3
Loading: A5
Loading: AN
Loading: C
Loading: C3
Loading: C5
Loading: CN
Loading: DA
Loading: DA3
Loading: DA5
Loading: DAN
Loading: DC
Loading: DC3
Loading: DC5
Loading: DCN
Loading: DG
Loading: DG3
Loading: DG5
Loading: DGN
Loading: DT
Loading: DT3
Loading: DT5
Loading: DTN
Loading: G
Loading: G3
Loading: G5
Loading: GN
Loading: OHE
Loading: U
Loading: U3
Loading: U5
Loading: UN
>> #
>> #       Load water and ions
>> # 
>> loadOff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
>> loadOff solvents.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: MEOHBOX
Loading: NMABOX
Loading: OPC
Loading: OPCBOX
Loading: PL3
Loading: POL3BOX
Loading: QSPCFWBOX
Loading: SPC
Loading: SPCBOX
Loading: SPCFWBOX
Loading: SPF
Loading: SPG
Loading: T4E
Loading: TIP3PBOX
Loading: TIP3PFBOX
Loading: TIP4PBOX
Loading: TIP4PEWBOX
Loading: TIP5PBOX
Loading: TP3
Loading: TP4
Loading: TP5
Loading: TPF
>> HOH = TP3
>> WAT = TP3
>> 
>> #
>> #	Define the PDB name map for the amino acids and nucleic acids
>> #     (note: no NHYP!  use neutral form for now)
>> #
>> addPdbResMap {
>>   { 0 "HYP" "HYP"  } { 1 "HYP" "CHYP" }
>>   { 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
>>   { 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
>>   { 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
>>   { 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
>>   { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
>>   { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
>>   { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
>>   { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
>>   { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
>>   { 0 "HID" "NHID" } { 1 "HID" "CHID" }
>>   { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
>>   { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
>>   { 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
>>   { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
>>   { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
>>   { 0 "MET" "NMET" } { 1 "MET" "CMET" }
>>   { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
>>   { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
>>   { 0 "SER" "NSER" } { 1 "SER" "CSER" }
>>   { 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
>>   { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
>>   { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
>>   { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
>>   { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
>>   { 0 "G" "G5"  } { 1 "G" "G3"  } 
>>   { 0 "A" "A5"  } { 1 "A" "A3"  } 
>>   { 0 "C" "C5"  } { 1 "C" "C3"  } 
>>   { 0 "U" "U5"  } { 1 "U" "U3"  } 
>>   { 0 "DG" "DG5"  } { 1 "DG" "DG3"  }  
>>   { 0 "DA" "DA5"  } { 1 "DA" "DA3"  }  
>>   { 0 "DC" "DC5"  } { 1 "DC" "DC3"  }  
>>   { 0 "DT" "DT5"  } { 1 "DT" "DT3"  }  
>> #  some old Amber residue names for RNA:
>>   { 0  "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" }
>>   { 0  "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" }
>>   { 0  "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" }
>>   { 0  "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" }
>> #  some really old Amber residue names, assuming DNA:
>>   { 0 "GUA" "DG5"  } { 1 "GUA" "DG3"  } { "GUA" "DG" }
>>   { 0 "ADE" "DA5"  } { 1 "ADE" "DA3"  } { "ADE" "DA" }
>>   { 0 "CYT" "DC5"  } { 1 "CYT" "DC3"  } { "CYT" "DC" }
>>   { 0 "THY" "DT5"  } { 1 "THY" "DT3"  } { "THY" "DT" }
>> #  uncomment out the following if you have this old style RNA files:
>> # { 0 "GUA" "G5"  } { 1 "GUA" "G3"  } { "GUA" "G" }
>> # { 0 "ADE" "A5"  } { 1 "ADE" "A3"  } { "ADE" "A" }
>> # { 0 "CYT" "C5"  } { 1 "CYT" "C3"  } { "CYT" "C" }
>> # { 0 "URA" "R5"  } { 1 "URA" "R3"  } { "URA" "R" }
>> 
>> }
>> 
>> #  try to be good about reading in really old atom names as well:
>> addPdbAtomMap {
>>   { "O5*" "O5'" }
>>   { "C5*" "C5'" }
>>   { "C4*" "C4'" }
>>   { "O4*" "O4'" }
>>   { "C3*" "C3'" }
>>   { "O3*" "O3'" }
>>   { "C2*" "C2'" }
>>   { "O2*" "O2'" }
>>   { "C1*" "C1'" }
>>   { "C5M" "C7"  }
>>   { "H1*" "H1'" }
>>   { "H2*1" "H2'" }
>>   { "H2*2" "H2''" }
>>   { "HO*2" "HO2'" }
>>   { "H2'1" "H2'" }
>>   { "H2'2" "H2''" }
>>   { "H3*" "H3'" }
>>   { "H4*" "H4'" }
>>   { "H5*1" "H5'" }
>>   { "H5*2" "H5''" }
>>   { "H5'1" "H5'" }
>>   { "H5'2" "H5''" }
>>   { "HO'2" "HO2'" }
>>   { "H5T"  "HO5'" }
>>   { "H3T"  "HO3'" }
>>   { "O1'" "O4'" }
>>   { "OA"  "OP1" }
>>   { "OB"  "OP2" }
>>   { "O1P" "OP1" }
>>   { "O2P" "OP2" }
>> }
>> 
>> #
>> # assume that most often proteins use HIE
>> #
>> NHIS = NHIE
>> HIS = HIE
>> CHIS = CHIE
> 
> loadoff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
> loadamberparams frcmod.opc
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.opc
Reading force field modification type file (frcmod)
Reading title:
Parameters for OPC water (JPCL, 2014, 5 (21), pp 3863–3871) 
(UNKNOWN ATOM TYPE: EP)
> loadamberparams frcmod.ionsjc_tip4pew
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip4pew
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP4P/EW water from Joung & Cheatham JPCB (2008)
> 
> m = loadpdb init.pdb
Loading PDB file: ./init.pdb
Enter zPdbReadScan from call depth  0.
Exit  zPdbReadScan from call depth  0.
Matching PDB residue names to LEaP variables.
(Residue 0: A5, Terminal/beginning, was not found in name map.)
(Residue 1: C3, Terminal/last, was not found in name map.)
Joining A5 - C3
  total atoms in file: 63
> 
> 
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.131155 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<H4' 9>
Warning: Close contact of 1.307451 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<C4' 8>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> solvatebox m OPCBOX 10.69 iso
  Solute vdw bounding box:              12.265 11.150 10.292
  Total bounding box for atom centers:  33.645 33.645 33.645
      (box expansion for 'iso' is   9.9%)
  Solvent unit box:                     18.865 18.478 19.006
The number of boxes:  x= 2  y= 2  z= 2
Adding box at: x=0  y=0  z=0
Center of solvent box is: 9.432422, 9.239054, 9.503120
Adding box at: x=0  y=0  z=1
Center of solvent box is: 9.432422, 9.239054, -9.503120
Adding box at: x=0  y=1  z=0
Center of solvent box is: 9.432422, -9.239054, 9.503120
Adding box at: x=0  y=1  z=1
Center of solvent box is: 9.432422, -9.239054, -9.503120
Adding box at: x=1  y=0  z=0
Center of solvent box is: -9.432422, 9.239054, 9.503120
Adding box at: x=1  y=0  z=1
Center of solvent box is: -9.432422, 9.239054, -9.503120
Adding box at: x=1  y=1  z=0
Center of solvent box is: -9.432422, -9.239054, 9.503120
Adding box at: x=1  y=1  z=1
Center of solvent box is: -9.432422, -9.239054, -9.503120
  Volume: 48626.484 A^3 
  Total mass 20172.840 amu,  Density 0.689 g/cc
  Added 1088 residues.
> quit
	Quit
log started: Sun Nov  1 20:53:04 2015

Log file: ./leap.log
>> #
>> # ----- leaprc for loading the ff12SB force field
>> # ----- NOTE: this is designed for PDB format 3!
>> #    Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA
>> #
>> #	load atom type hybridizations
>> #
>> addAtomTypes {
>> 	{ "H"   "H" "sp3" }
>> 	{ "HO"  "H" "sp3" }
>> 	{ "HS"  "H" "sp3" }
>> 	{ "H1"  "H" "sp3" }
>> 	{ "H2"  "H" "sp3" }
>> 	{ "H3"  "H" "sp3" }
>> 	{ "H4"  "H" "sp3" }
>> 	{ "H5"  "H" "sp3" }
>> 	{ "HW"  "H" "sp3" }
>> 	{ "HC"  "H" "sp3" }
>> 	{ "HA"  "H" "sp3" }
>> 	{ "HP"  "H" "sp3" }
>> 	{ "HZ"  "H" "sp3" }
>> 	{ "OH"  "O" "sp3" }
>> 	{ "OS"  "O" "sp3" }
>> 	{ "O"   "O" "sp2" }
>> 	{ "O2"  "O" "sp2" }
>> 	{ "OP"  "O" "sp2" }
>> 	{ "OW"  "O" "sp3" }
>> 	{ "CT"  "C" "sp3" }
>> 	{ "CX"  "C" "sp3" }
>> 	{ "C8"  "C" "sp3" }
>> 	{ "2C"  "C" "sp3" }
>> 	{ "3C"  "C" "sp3" }
>> 	{ "CH"  "C" "sp3" }
>> 	{ "CS"  "C" "sp2" }
>> 	{ "C"   "C" "sp2" }
>> 	{ "CO"   "C" "sp2" }
>> 	{ "C*"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CB"  "C" "sp2" }
>> 	{ "CC"  "C" "sp2" }
>> 	{ "CN"  "C" "sp2" }
>> 	{ "CM"  "C" "sp2" }
>> 	{ "CK"  "C" "sp2" }
>> 	{ "CQ"  "C" "sp2" }
>> 	{ "CD"  "C" "sp2" }
>> 	{ "C5"  "C" "sp2" }
>> 	{ "C4"  "C" "sp2" }
>> 	{ "CP"  "C" "sp2" }
>> 	{ "CI"  "C" "sp3" }
>> 	{ "CJ"  "C" "sp2" }
>> 	{ "CW"  "C" "sp2" }
>> 	{ "CV"  "C" "sp2" }
>> 	{ "CR"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CY"  "C" "sp2" }
>> 	{ "C0"  "Ca" "sp3" }
>> 	{ "MG"  "Mg" "sp3" }
>> 	{ "N"   "N" "sp2" }
>> 	{ "NA"  "N" "sp2" }
>> 	{ "N2"  "N" "sp2" }
>> 	{ "N*"  "N" "sp2" }
>> 	{ "NP"  "N" "sp2" }
>> 	{ "NQ"  "N" "sp2" }
>> 	{ "NB"  "N" "sp2" }
>> 	{ "NC"  "N" "sp2" }
>> 	{ "NT"  "N" "sp3" }
>> 	{ "NY"  "N" "sp2" }
>> 	{ "N3"  "N" "sp3" }
>> 	{ "S"   "S" "sp3" }
>> 	{ "SH"  "S" "sp3" }
>> 	{ "P"   "P" "sp3" }
>> 	{ "LP"  ""  "sp3" }
>> 	{ "EP"  ""  "sp3" }
>> 	{ "F"   "F" "sp3" }
>> 	{ "Cl"  "Cl" "sp3" }
>> 	{ "Br"  "Br" "sp3" }
>> 	{ "I"   "I"  "sp3" }
>> 	{ "F-"   "F" "sp3" }
>> 	{ "Cl-"  "Cl" "sp3" }
>> 	{ "Br-"  "Br" "sp3" }
>> 	{ "I-"   "I"  "sp3" }
>> 	{ "Li+"  "Li"  "sp3" }
>> 	{ "Na+"  "Na"  "sp3" }
>> 	{ "K+"  "K"  "sp3" }
>> 	{ "Rb+"  "Rb"  "sp3" }
>> 	{ "Cs+"  "Cs"  "sp3" }
>> 	{ "Mg+"  "Mg"  "sp3" }
>> # glycam
>> 	{ "OG"  "O" "sp3" }
>> 	{ "OL"  "O" "sp3" }
>> 	{ "AC"  "C" "sp3" }
>> 	{ "EC"  "C" "sp3" }
>> }
>> #
>> #	Load the main parameter set.
>> #
>> parm10 = loadamberparams parm10.dat
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
(UNKNOWN ATOM TYPE: Zn)
(UNKNOWN ATOM TYPE: EP)
>> frcmod12SB = loadamberparams frcmod.ff12SB
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff12SB
Reading force field modification type file (frcmod)
Reading title:
ff12SB protein backbone and sidechain parameters
>> #
>> #	Load main chain and terminating amino acid libraries, nucleic acids
>> #
>> loadOff amino12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/amino12.lib
Loading: ALA
Loading: ARG
Loading: ASH
Loading: ASN
Loading: ASP
Loading: CYM
Loading: CYS
Loading: CYX
Loading: GLH
Loading: GLN
Loading: GLU
Loading: GLY
Loading: HID
Loading: HIE
Loading: HIP
Loading: HYP
Loading: ILE
Loading: LEU
Loading: LYN
Loading: LYS
Loading: MET
Loading: PHE
Loading: PRO
Loading: SER
Loading: THR
Loading: TRP
Loading: TYR
Loading: VAL
>> loadOff aminoct12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminoct12.lib
Loading: CALA
Loading: CARG
Loading: CASN
Loading: CASP
Loading: CCYS
Loading: CCYX
Loading: CGLN
Loading: CGLU
Loading: CGLY
Loading: CHID
Loading: CHIE
Loading: CHIP
Loading: CHYP
Loading: CILE
Loading: CLEU
Loading: CLYS
Loading: CMET
Loading: CPHE
Loading: CPRO
Loading: CSER
Loading: CTHR
Loading: CTRP
Loading: CTYR
Loading: CVAL
Loading: NHE
Loading: NME
>> loadOff aminont12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminont12.lib
Loading: ACE
Loading: NALA
Loading: NARG
Loading: NASN
Loading: NASP
Loading: NCYS
Loading: NCYX
Loading: NGLN
Loading: NGLU
Loading: NGLY
Loading: NHID
Loading: NHIE
Loading: NHIP
Loading: NILE
Loading: NLEU
Loading: NLYS
Loading: NMET
Loading: NPHE
Loading: NPRO
Loading: NSER
Loading: NTHR
Loading: NTRP
Loading: NTYR
Loading: NVAL
>> loadOff nucleic12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/nucleic12.lib
Loading: A
Loading: A3
Loading: A5
Loading: AN
Loading: C
Loading: C3
Loading: C5
Loading: CN
Loading: DA
Loading: DA3
Loading: DA5
Loading: DAN
Loading: DC
Loading: DC3
Loading: DC5
Loading: DCN
Loading: DG
Loading: DG3
Loading: DG5
Loading: DGN
Loading: DT
Loading: DT3
Loading: DT5
Loading: DTN
Loading: G
Loading: G3
Loading: G5
Loading: GN
Loading: OHE
Loading: U
Loading: U3
Loading: U5
Loading: UN
>> #
>> #       Load water and ions
>> # 
>> loadOff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
>> loadOff solvents.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: MEOHBOX
Loading: NMABOX
Loading: OPC
Loading: OPCBOX
Loading: PL3
Loading: POL3BOX
Loading: QSPCFWBOX
Loading: SPC
Loading: SPCBOX
Loading: SPCFWBOX
Loading: SPF
Loading: SPG
Loading: T4E
Loading: TIP3PBOX
Loading: TIP3PFBOX
Loading: TIP4PBOX
Loading: TIP4PEWBOX
Loading: TIP5PBOX
Loading: TP3
Loading: TP4
Loading: TP5
Loading: TPF
>> HOH = TP3
>> WAT = TP3
>> 
>> #
>> #	Define the PDB name map for the amino acids and nucleic acids
>> #     (note: no NHYP!  use neutral form for now)
>> #
>> addPdbResMap {
>>   { 0 "HYP" "HYP"  } { 1 "HYP" "CHYP" }
>>   { 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
>>   { 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
>>   { 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
>>   { 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
>>   { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
>>   { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
>>   { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
>>   { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
>>   { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
>>   { 0 "HID" "NHID" } { 1 "HID" "CHID" }
>>   { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
>>   { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
>>   { 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
>>   { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
>>   { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
>>   { 0 "MET" "NMET" } { 1 "MET" "CMET" }
>>   { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
>>   { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
>>   { 0 "SER" "NSER" } { 1 "SER" "CSER" }
>>   { 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
>>   { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
>>   { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
>>   { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
>>   { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
>>   { 0 "G" "G5"  } { 1 "G" "G3"  } 
>>   { 0 "A" "A5"  } { 1 "A" "A3"  } 
>>   { 0 "C" "C5"  } { 1 "C" "C3"  } 
>>   { 0 "U" "U5"  } { 1 "U" "U3"  } 
>>   { 0 "DG" "DG5"  } { 1 "DG" "DG3"  }  
>>   { 0 "DA" "DA5"  } { 1 "DA" "DA3"  }  
>>   { 0 "DC" "DC5"  } { 1 "DC" "DC3"  }  
>>   { 0 "DT" "DT5"  } { 1 "DT" "DT3"  }  
>> #  some old Amber residue names for RNA:
>>   { 0  "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" }
>>   { 0  "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" }
>>   { 0  "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" }
>>   { 0  "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" }
>> #  some really old Amber residue names, assuming DNA:
>>   { 0 "GUA" "DG5"  } { 1 "GUA" "DG3"  } { "GUA" "DG" }
>>   { 0 "ADE" "DA5"  } { 1 "ADE" "DA3"  } { "ADE" "DA" }
>>   { 0 "CYT" "DC5"  } { 1 "CYT" "DC3"  } { "CYT" "DC" }
>>   { 0 "THY" "DT5"  } { 1 "THY" "DT3"  } { "THY" "DT" }
>> #  uncomment out the following if you have this old style RNA files:
>> # { 0 "GUA" "G5"  } { 1 "GUA" "G3"  } { "GUA" "G" }
>> # { 0 "ADE" "A5"  } { 1 "ADE" "A3"  } { "ADE" "A" }
>> # { 0 "CYT" "C5"  } { 1 "CYT" "C3"  } { "CYT" "C" }
>> # { 0 "URA" "R5"  } { 1 "URA" "R3"  } { "URA" "R" }
>> 
>> }
>> 
>> #  try to be good about reading in really old atom names as well:
>> addPdbAtomMap {
>>   { "O5*" "O5'" }
>>   { "C5*" "C5'" }
>>   { "C4*" "C4'" }
>>   { "O4*" "O4'" }
>>   { "C3*" "C3'" }
>>   { "O3*" "O3'" }
>>   { "C2*" "C2'" }
>>   { "O2*" "O2'" }
>>   { "C1*" "C1'" }
>>   { "C5M" "C7"  }
>>   { "H1*" "H1'" }
>>   { "H2*1" "H2'" }
>>   { "H2*2" "H2''" }
>>   { "HO*2" "HO2'" }
>>   { "H2'1" "H2'" }
>>   { "H2'2" "H2''" }
>>   { "H3*" "H3'" }
>>   { "H4*" "H4'" }
>>   { "H5*1" "H5'" }
>>   { "H5*2" "H5''" }
>>   { "H5'1" "H5'" }
>>   { "H5'2" "H5''" }
>>   { "HO'2" "HO2'" }
>>   { "H5T"  "HO5'" }
>>   { "H3T"  "HO3'" }
>>   { "O1'" "O4'" }
>>   { "OA"  "OP1" }
>>   { "OB"  "OP2" }
>>   { "O1P" "OP1" }
>>   { "O2P" "OP2" }
>> }
>> 
>> #
>> # assume that most often proteins use HIE
>> #
>> NHIS = NHIE
>> HIS = HIE
>> CHIS = CHIE
> 
> loadoff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
> loadamberparams frcmod.opc
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.opc
Reading force field modification type file (frcmod)
Reading title:
Parameters for OPC water (JPCL, 2014, 5 (21), pp 3863–3871) 
(UNKNOWN ATOM TYPE: EP)
> loadamberparams frcmod.ionsjc_tip4pew
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip4pew
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP4P/EW water from Joung & Cheatham JPCB (2008)
> 
> m = loadpdb init.pdb
Loading PDB file: ./init.pdb
Enter zPdbReadScan from call depth  0.
Exit  zPdbReadScan from call depth  0.
Matching PDB residue names to LEaP variables.
(Residue 0: A5, Terminal/beginning, was not found in name map.)
(Residue 1: C3, Terminal/last, was not found in name map.)
Joining A5 - C3
  total atoms in file: 63
> 
> 
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.131155 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<H4' 9>
Warning: Close contact of 1.307451 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<C4' 8>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> solvateoct m OPCBOX 10.69 iso
Scaling up box by a factor of 1.255308 to meet diagonal cut criterion
  Solute vdw bounding box:              12.265 11.150 10.292
  Total bounding box for atom centers:  39.103 39.103 39.103
      (box expansion for 'iso' is   8.4%)
  Solvent unit box:                     18.865 18.478 19.006
The number of boxes:  x= 3  y= 3  z= 3
Adding box at: x=0  y=0  z=0
Center of solvent box is: 18.864844, 18.478108, 19.006241
Adding box at: x=0  y=0  z=1
Center of solvent box is: 18.864844, 18.478108, 0.000000
Adding box at: x=0  y=0  z=2
Center of solvent box is: 18.864844, 18.478108, -19.006241
Adding box at: x=0  y=1  z=0
Center of solvent box is: 18.864844, 0.000000, 19.006241
Adding box at: x=0  y=1  z=1
Center of solvent box is: 18.864844, 0.000000, 0.000000
Adding box at: x=0  y=1  z=2
Center of solvent box is: 18.864844, 0.000000, -19.006241
Adding box at: x=0  y=2  z=0
Center of solvent box is: 18.864844, -18.478108, 19.006241
Adding box at: x=0  y=2  z=1
Center of solvent box is: 18.864844, -18.478108, 0.000000
Adding box at: x=0  y=2  z=2
Center of solvent box is: 18.864844, -18.478108, -19.006241
Adding box at: x=1  y=0  z=0
Center of solvent box is: 0.000000, 18.478108, 19.006241
Adding box at: x=1  y=0  z=1
Center of solvent box is: 0.000000, 18.478108, 0.000000
Adding box at: x=1  y=0  z=2
Center of solvent box is: 0.000000, 18.478108, -19.006241
Adding box at: x=1  y=1  z=0
Center of solvent box is: 0.000000, 0.000000, 19.006241
Adding box at: x=1  y=1  z=1
Center of solvent box is: 0.000000, 0.000000, 0.000000
Adding box at: x=1  y=1  z=2
Center of solvent box is: 0.000000, 0.000000, -19.006241
Adding box at: x=1  y=2  z=0
Center of solvent box is: 0.000000, -18.478108, 19.006241
Adding box at: x=1  y=2  z=1
Center of solvent box is: 0.000000, -18.478108, 0.000000
Adding box at: x=1  y=2  z=2
Center of solvent box is: 0.000000, -18.478108, -19.006241
Adding box at: x=2  y=0  z=0
Center of solvent box is: -18.864844, 18.478108, 19.006241
Adding box at: x=2  y=0  z=1
Center of solvent box is: -18.864844, 18.478108, 0.000000
Adding box at: x=2  y=0  z=2
Center of solvent box is: -18.864844, 18.478108, -19.006241
Adding box at: x=2  y=1  z=0
Center of solvent box is: -18.864844, 0.000000, 19.006241
Adding box at: x=2  y=1  z=1
Center of solvent box is: -18.864844, 0.000000, 0.000000
Adding box at: x=2  y=1  z=2
Center of solvent box is: -18.864844, 0.000000, -19.006241
Adding box at: x=2  y=2  z=0
Center of solvent box is: -18.864844, -18.478108, 19.006241
Adding box at: x=2  y=2  z=1
Center of solvent box is: -18.864844, -18.478108, 0.000000
Adding box at: x=2  y=2  z=2
Center of solvent box is: -18.864844, -18.478108, -19.006241
  Volume: 32248.128 A^3 (oct)
  Total mass 16083.208 amu,  Density 0.828 g/cc
  Added 861 residues.
> remove m m.1090
remove: Argument #2 is type String must be of type: [molecule residue atom]
usage:  remove <unit/residue/atom> <unit/residue/atom>
> remove m m.1089
remove: Argument #2 is type String must be of type: [molecule residue atom]
usage:  remove <unit/residue/atom> <unit/residue/atom>
> 
> addions m Na+ 0
1 Na+ ion required to neutralize.
Adding 1 counter ions to "m" using 1A grid
Total solute charge:  -1.00  Max atom radius:   2.10
Grid extends from solute vdw + 1.23  to  7.33
Box:
   enclosing:  -12.20 -12.49 -11.97   11.09 10.82 11.63
   sized:			      19.80 19.51 20.03
   edge:        32.00
Resolution:      1.00 Angstrom.
Tree depth: 5
grid build: 0 sec
Volume = 15.67% of box, grid points 5136
Solvent present: replacing closest with ion
	 when steric overlaps occur
Calculating grid charges
charges: 0 sec
(Replacing solvent molecule)
Placed Na+ in m at (-4.38, 7.25, -4.38).

Done adding ions.
> addions m Na+ 5 Cl- 5
Na+ has a charge of 0.
Adding the ions anyway.
Adding 10 counter ions to "m" using 1A grid
Total solute charge:   0.00  Max atom radius:   2.10
Grid extends from solute vdw + 6.14  to  12.24
Box:
   enclosing:  -17.11 -17.40 -16.88   16.00 19.48 16.54
   sized:			      46.89 46.60 47.12
   edge:        64.00
Resolution:      1.00 Angstrom.
Tree depth: 6
grid build: 0 sec
Volume =  5.01% of box, grid points 13140
Solvent present: replacing closest with ion
	 when steric overlaps occur
Calculating grid charges
charges: 0 sec
(Replacing solvent molecule)
Placed Na+ in m at (-4.73, -8.56, -3.11).
(Replacing solvent molecule)
Placed Cl- in m at (-2.50, -14.15, -4.83).
(Replacing solvent molecule)
Placed Na+ in m at (-1.01, -11.40, -1.44).
(Replacing solvent molecule)
Placed Cl- in m at (-5.34, -11.16, 0.85).
(Replacing solvent molecule)
Placed Na+ in m at (-1.46, -11.96, -6.99).
(Replacing solvent molecule)
Placed Cl- in m at (3.03, -11.69, -4.89).
(Replacing solvent molecule)
Placed Na+ in m at (7.30, -13.44, -5.41).
(Replacing solvent molecule)
Placed Cl- in m at (2.44, -10.48, -7.61).
(Replacing solvent molecule)
Placed Na+ in m at (4.31, -8.53, -6.37).
(Replacing solvent molecule)
Placed Cl- in m at (11.17, -9.60, -6.59).

Done adding ions.
> 
> saveamberparm m full.topo non-randomized.crds
Checking Unit.

 -- ignoring the warnings.

Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 ** Warning: No sp2 improper torsion term for  N*-CB-CB-NC
        atoms are: N9 C5 C4 N3
 ** Warning: No sp2 improper torsion term for  NB-CA-CB-CB
        atoms are: N7 C6 C5 C4
 total 11 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
 (no restraints)
> quit
	Quit
log started: Sun Nov  1 20:53:05 2015

Log file: ./leap.log
>> #
>> # ----- leaprc for loading the ff12SB force field
>> # ----- NOTE: this is designed for PDB format 3!
>> #    Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA
>> #
>> #	load atom type hybridizations
>> #
>> addAtomTypes {
>> 	{ "H"   "H" "sp3" }
>> 	{ "HO"  "H" "sp3" }
>> 	{ "HS"  "H" "sp3" }
>> 	{ "H1"  "H" "sp3" }
>> 	{ "H2"  "H" "sp3" }
>> 	{ "H3"  "H" "sp3" }
>> 	{ "H4"  "H" "sp3" }
>> 	{ "H5"  "H" "sp3" }
>> 	{ "HW"  "H" "sp3" }
>> 	{ "HC"  "H" "sp3" }
>> 	{ "HA"  "H" "sp3" }
>> 	{ "HP"  "H" "sp3" }
>> 	{ "HZ"  "H" "sp3" }
>> 	{ "OH"  "O" "sp3" }
>> 	{ "OS"  "O" "sp3" }
>> 	{ "O"   "O" "sp2" }
>> 	{ "O2"  "O" "sp2" }
>> 	{ "OP"  "O" "sp2" }
>> 	{ "OW"  "O" "sp3" }
>> 	{ "CT"  "C" "sp3" }
>> 	{ "CX"  "C" "sp3" }
>> 	{ "C8"  "C" "sp3" }
>> 	{ "2C"  "C" "sp3" }
>> 	{ "3C"  "C" "sp3" }
>> 	{ "CH"  "C" "sp3" }
>> 	{ "CS"  "C" "sp2" }
>> 	{ "C"   "C" "sp2" }
>> 	{ "CO"   "C" "sp2" }
>> 	{ "C*"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CB"  "C" "sp2" }
>> 	{ "CC"  "C" "sp2" }
>> 	{ "CN"  "C" "sp2" }
>> 	{ "CM"  "C" "sp2" }
>> 	{ "CK"  "C" "sp2" }
>> 	{ "CQ"  "C" "sp2" }
>> 	{ "CD"  "C" "sp2" }
>> 	{ "C5"  "C" "sp2" }
>> 	{ "C4"  "C" "sp2" }
>> 	{ "CP"  "C" "sp2" }
>> 	{ "CI"  "C" "sp3" }
>> 	{ "CJ"  "C" "sp2" }
>> 	{ "CW"  "C" "sp2" }
>> 	{ "CV"  "C" "sp2" }
>> 	{ "CR"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CY"  "C" "sp2" }
>> 	{ "C0"  "Ca" "sp3" }
>> 	{ "MG"  "Mg" "sp3" }
>> 	{ "N"   "N" "sp2" }
>> 	{ "NA"  "N" "sp2" }
>> 	{ "N2"  "N" "sp2" }
>> 	{ "N*"  "N" "sp2" }
>> 	{ "NP"  "N" "sp2" }
>> 	{ "NQ"  "N" "sp2" }
>> 	{ "NB"  "N" "sp2" }
>> 	{ "NC"  "N" "sp2" }
>> 	{ "NT"  "N" "sp3" }
>> 	{ "NY"  "N" "sp2" }
>> 	{ "N3"  "N" "sp3" }
>> 	{ "S"   "S" "sp3" }
>> 	{ "SH"  "S" "sp3" }
>> 	{ "P"   "P" "sp3" }
>> 	{ "LP"  ""  "sp3" }
>> 	{ "EP"  ""  "sp3" }
>> 	{ "F"   "F" "sp3" }
>> 	{ "Cl"  "Cl" "sp3" }
>> 	{ "Br"  "Br" "sp3" }
>> 	{ "I"   "I"  "sp3" }
>> 	{ "F-"   "F" "sp3" }
>> 	{ "Cl-"  "Cl" "sp3" }
>> 	{ "Br-"  "Br" "sp3" }
>> 	{ "I-"   "I"  "sp3" }
>> 	{ "Li+"  "Li"  "sp3" }
>> 	{ "Na+"  "Na"  "sp3" }
>> 	{ "K+"  "K"  "sp3" }
>> 	{ "Rb+"  "Rb"  "sp3" }
>> 	{ "Cs+"  "Cs"  "sp3" }
>> 	{ "Mg+"  "Mg"  "sp3" }
>> # glycam
>> 	{ "OG"  "O" "sp3" }
>> 	{ "OL"  "O" "sp3" }
>> 	{ "AC"  "C" "sp3" }
>> 	{ "EC"  "C" "sp3" }
>> }
>> #
>> #	Load the main parameter set.
>> #
>> parm10 = loadamberparams parm10.dat
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
(UNKNOWN ATOM TYPE: Zn)
(UNKNOWN ATOM TYPE: EP)
>> frcmod12SB = loadamberparams frcmod.ff12SB
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff12SB
Reading force field modification type file (frcmod)
Reading title:
ff12SB protein backbone and sidechain parameters
>> #
>> #	Load main chain and terminating amino acid libraries, nucleic acids
>> #
>> loadOff amino12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/amino12.lib
Loading: ALA
Loading: ARG
Loading: ASH
Loading: ASN
Loading: ASP
Loading: CYM
Loading: CYS
Loading: CYX
Loading: GLH
Loading: GLN
Loading: GLU
Loading: GLY
Loading: HID
Loading: HIE
Loading: HIP
Loading: HYP
Loading: ILE
Loading: LEU
Loading: LYN
Loading: LYS
Loading: MET
Loading: PHE
Loading: PRO
Loading: SER
Loading: THR
Loading: TRP
Loading: TYR
Loading: VAL
>> loadOff aminoct12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminoct12.lib
Loading: CALA
Loading: CARG
Loading: CASN
Loading: CASP
Loading: CCYS
Loading: CCYX
Loading: CGLN
Loading: CGLU
Loading: CGLY
Loading: CHID
Loading: CHIE
Loading: CHIP
Loading: CHYP
Loading: CILE
Loading: CLEU
Loading: CLYS
Loading: CMET
Loading: CPHE
Loading: CPRO
Loading: CSER
Loading: CTHR
Loading: CTRP
Loading: CTYR
Loading: CVAL
Loading: NHE
Loading: NME
>> loadOff aminont12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminont12.lib
Loading: ACE
Loading: NALA
Loading: NARG
Loading: NASN
Loading: NASP
Loading: NCYS
Loading: NCYX
Loading: NGLN
Loading: NGLU
Loading: NGLY
Loading: NHID
Loading: NHIE
Loading: NHIP
Loading: NILE
Loading: NLEU
Loading: NLYS
Loading: NMET
Loading: NPHE
Loading: NPRO
Loading: NSER
Loading: NTHR
Loading: NTRP
Loading: NTYR
Loading: NVAL
>> loadOff nucleic12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/nucleic12.lib
Loading: A
Loading: A3
Loading: A5
Loading: AN
Loading: C
Loading: C3
Loading: C5
Loading: CN
Loading: DA
Loading: DA3
Loading: DA5
Loading: DAN
Loading: DC
Loading: DC3
Loading: DC5
Loading: DCN
Loading: DG
Loading: DG3
Loading: DG5
Loading: DGN
Loading: DT
Loading: DT3
Loading: DT5
Loading: DTN
Loading: G
Loading: G3
Loading: G5
Loading: GN
Loading: OHE
Loading: U
Loading: U3
Loading: U5
Loading: UN
>> #
>> #       Load water and ions
>> # 
>> loadOff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
>> loadOff solvents.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: MEOHBOX
Loading: NMABOX
Loading: OPC
Loading: OPCBOX
Loading: PL3
Loading: POL3BOX
Loading: QSPCFWBOX
Loading: SPC
Loading: SPCBOX
Loading: SPCFWBOX
Loading: SPF
Loading: SPG
Loading: T4E
Loading: TIP3PBOX
Loading: TIP3PFBOX
Loading: TIP4PBOX
Loading: TIP4PEWBOX
Loading: TIP5PBOX
Loading: TP3
Loading: TP4
Loading: TP5
Loading: TPF
>> HOH = TP3
>> WAT = TP3
>> 
>> #
>> #	Define the PDB name map for the amino acids and nucleic acids
>> #     (note: no NHYP!  use neutral form for now)
>> #
>> addPdbResMap {
>>   { 0 "HYP" "HYP"  } { 1 "HYP" "CHYP" }
>>   { 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
>>   { 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
>>   { 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
>>   { 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
>>   { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
>>   { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
>>   { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
>>   { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
>>   { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
>>   { 0 "HID" "NHID" } { 1 "HID" "CHID" }
>>   { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
>>   { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
>>   { 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
>>   { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
>>   { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
>>   { 0 "MET" "NMET" } { 1 "MET" "CMET" }
>>   { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
>>   { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
>>   { 0 "SER" "NSER" } { 1 "SER" "CSER" }
>>   { 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
>>   { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
>>   { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
>>   { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
>>   { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
>>   { 0 "G" "G5"  } { 1 "G" "G3"  } 
>>   { 0 "A" "A5"  } { 1 "A" "A3"  } 
>>   { 0 "C" "C5"  } { 1 "C" "C3"  } 
>>   { 0 "U" "U5"  } { 1 "U" "U3"  } 
>>   { 0 "DG" "DG5"  } { 1 "DG" "DG3"  }  
>>   { 0 "DA" "DA5"  } { 1 "DA" "DA3"  }  
>>   { 0 "DC" "DC5"  } { 1 "DC" "DC3"  }  
>>   { 0 "DT" "DT5"  } { 1 "DT" "DT3"  }  
>> #  some old Amber residue names for RNA:
>>   { 0  "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" }
>>   { 0  "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" }
>>   { 0  "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" }
>>   { 0  "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" }
>> #  some really old Amber residue names, assuming DNA:
>>   { 0 "GUA" "DG5"  } { 1 "GUA" "DG3"  } { "GUA" "DG" }
>>   { 0 "ADE" "DA5"  } { 1 "ADE" "DA3"  } { "ADE" "DA" }
>>   { 0 "CYT" "DC5"  } { 1 "CYT" "DC3"  } { "CYT" "DC" }
>>   { 0 "THY" "DT5"  } { 1 "THY" "DT3"  } { "THY" "DT" }
>> #  uncomment out the following if you have this old style RNA files:
>> # { 0 "GUA" "G5"  } { 1 "GUA" "G3"  } { "GUA" "G" }
>> # { 0 "ADE" "A5"  } { 1 "ADE" "A3"  } { "ADE" "A" }
>> # { 0 "CYT" "C5"  } { 1 "CYT" "C3"  } { "CYT" "C" }
>> # { 0 "URA" "R5"  } { 1 "URA" "R3"  } { "URA" "R" }
>> 
>> }
>> 
>> #  try to be good about reading in really old atom names as well:
>> addPdbAtomMap {
>>   { "O5*" "O5'" }
>>   { "C5*" "C5'" }
>>   { "C4*" "C4'" }
>>   { "O4*" "O4'" }
>>   { "C3*" "C3'" }
>>   { "O3*" "O3'" }
>>   { "C2*" "C2'" }
>>   { "O2*" "O2'" }
>>   { "C1*" "C1'" }
>>   { "C5M" "C7"  }
>>   { "H1*" "H1'" }
>>   { "H2*1" "H2'" }
>>   { "H2*2" "H2''" }
>>   { "HO*2" "HO2'" }
>>   { "H2'1" "H2'" }
>>   { "H2'2" "H2''" }
>>   { "H3*" "H3'" }
>>   { "H4*" "H4'" }
>>   { "H5*1" "H5'" }
>>   { "H5*2" "H5''" }
>>   { "H5'1" "H5'" }
>>   { "H5'2" "H5''" }
>>   { "HO'2" "HO2'" }
>>   { "H5T"  "HO5'" }
>>   { "H3T"  "HO3'" }
>>   { "O1'" "O4'" }
>>   { "OA"  "OP1" }
>>   { "OB"  "OP2" }
>>   { "O1P" "OP1" }
>>   { "O2P" "OP2" }
>> }
>> 
>> #
>> # assume that most often proteins use HIE
>> #
>> NHIS = NHIE
>> HIS = HIE
>> CHIS = CHIE
> 
> loadoff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
> loadamberparams frcmod.opc
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.opc
Reading force field modification type file (frcmod)
Reading title:
Parameters for OPC water (JPCL, 2014, 5 (21), pp 3863–3871) 
(UNKNOWN ATOM TYPE: EP)
> loadamberparams frcmod.ionsjc_tip4pew
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip4pew
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP4P/EW water from Joung & Cheatham JPCB (2008)
> 
> m = loadpdb init.pdb
Loading PDB file: ./init.pdb
Enter zPdbReadScan from call depth  0.
Exit  zPdbReadScan from call depth  0.
Matching PDB residue names to LEaP variables.
(Residue 0: A5, Terminal/beginning, was not found in name map.)
(Residue 1: C3, Terminal/last, was not found in name map.)
Joining A5 - C3
  total atoms in file: 63
> 
> 
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.131155 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<H4' 9>
Warning: Close contact of 1.307451 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<C4' 8>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> solvatebox m OPCBOX 10.69 iso
  Solute vdw bounding box:              12.265 11.150 10.292
  Total bounding box for atom centers:  33.645 33.645 33.645
      (box expansion for 'iso' is   9.9%)
  Solvent unit box:                     18.865 18.478 19.006
The number of boxes:  x= 2  y= 2  z= 2
Adding box at: x=0  y=0  z=0
Center of solvent box is: 9.432422, 9.239054, 9.503120
Adding box at: x=0  y=0  z=1
Center of solvent box is: 9.432422, 9.239054, -9.503120
Adding box at: x=0  y=1  z=0
Center of solvent box is: 9.432422, -9.239054, 9.503120
Adding box at: x=0  y=1  z=1
Center of solvent box is: 9.432422, -9.239054, -9.503120
Adding box at: x=1  y=0  z=0
Center of solvent box is: -9.432422, 9.239054, 9.503120
Adding box at: x=1  y=0  z=1
Center of solvent box is: -9.432422, 9.239054, -9.503120
Adding box at: x=1  y=1  z=0
Center of solvent box is: -9.432422, -9.239054, 9.503120
Adding box at: x=1  y=1  z=1
Center of solvent box is: -9.432422, -9.239054, -9.503120
  Volume: 48626.484 A^3 
  Total mass 20172.840 amu,  Density 0.689 g/cc
  Added 1088 residues.
> remove m m.1090
> remove m m.1089
> 
> addions m Na+ 0
1 Na+ ion required to neutralize.
Adding 1 counter ions to "m" using 1A grid
Total solute charge:  -1.00  Max atom radius:   2.10
Grid extends from solute vdw + 1.23  to  7.33
Box:
   enclosing:  -11.90 -11.84 -11.12   12.54 11.31 11.09
   sized:			      20.10 20.16 20.88
   edge:        32.00
Resolution:      1.00 Angstrom.
Tree depth: 5
grid build: 0 sec
Volume = 15.67% of box, grid points 5135
Solvent present: replacing closest with ion
	 when steric overlaps occur
Calculating grid charges
charges: 0 sec
(Replacing solvent molecule)
Placed Na+ in m at (-5.98, 4.85, -2.80).

Done adding ions.
> addions m Na+ 5 Cl- 5
Na+ has a charge of 0.
Adding the ions anyway.
Adding 10 counter ions to "m" using 1A grid
Total solute charge:   0.00  Max atom radius:   2.10
Grid extends from solute vdw + 6.14  to  12.24
Box:
   enclosing:  -18.22 -16.75 -16.03   17.46 17.09 16.00
   sized:			      45.78 47.25 47.97
   edge:        64.00
Resolution:      1.00 Angstrom.
Tree depth: 6
grid build: 0 sec
Volume =  4.90% of box, grid points 12839
Solvent present: replacing closest with ion
	 when steric overlaps occur
Calculating grid charges
charges: 0 sec
(Replacing solvent molecule)
Placed Na+ in m at (-0.14, -3.24, 9.75).
(Replacing solvent molecule)
Placed Cl- in m at (2.85, -0.93, 8.58).
(Replacing solvent molecule)
Placed Na+ in m at (8.07, 1.13, 7.86).
(Replacing solvent molecule)
Placed Cl- in m at (-0.46, 0.47, 14.00).
(Replacing solvent molecule)
Placed Na+ in m at (3.98, 1.37, 9.85).
(Replacing solvent molecule)
Placed Cl- in m at (8.42, 0.74, 10.66).
(Replacing solvent molecule)
Placed Na+ in m at (1.80, 4.34, 13.61).
(Replacing solvent molecule)
Placed Cl- in m at (4.87, 5.75, 10.61).
(Replacing solvent molecule)
Placed Na+ in m at (7.00, 4.40, 11.69).
(Replacing solvent molecule)
Placed Cl- in m at (3.61, 1.92, 13.32).

Done adding ions.
> 
> saveamberparm m full.topo non-randomized.crds
Checking Unit.

 -- ignoring the warnings.

Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 ** Warning: No sp2 improper torsion term for  N*-CB-CB-NC
        atoms are: N9 C5 C4 N3
 ** Warning: No sp2 improper torsion term for  NB-CA-CB-CB
        atoms are: N7 C6 C5 C4
 total 11 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
 (no restraints)
> quit
	Quit
log started: Sun Nov  1 20:53:05 2015

Log file: ./leap.log
>> #
>> # ----- leaprc for loading the ff12SB force field
>> # ----- NOTE: this is designed for PDB format 3!
>> #    Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA
>> #
>> #	load atom type hybridizations
>> #
>> addAtomTypes {
>> 	{ "H"   "H" "sp3" }
>> 	{ "HO"  "H" "sp3" }
>> 	{ "HS"  "H" "sp3" }
>> 	{ "H1"  "H" "sp3" }
>> 	{ "H2"  "H" "sp3" }
>> 	{ "H3"  "H" "sp3" }
>> 	{ "H4"  "H" "sp3" }
>> 	{ "H5"  "H" "sp3" }
>> 	{ "HW"  "H" "sp3" }
>> 	{ "HC"  "H" "sp3" }
>> 	{ "HA"  "H" "sp3" }
>> 	{ "HP"  "H" "sp3" }
>> 	{ "HZ"  "H" "sp3" }
>> 	{ "OH"  "O" "sp3" }
>> 	{ "OS"  "O" "sp3" }
>> 	{ "O"   "O" "sp2" }
>> 	{ "O2"  "O" "sp2" }
>> 	{ "OP"  "O" "sp2" }
>> 	{ "OW"  "O" "sp3" }
>> 	{ "CT"  "C" "sp3" }
>> 	{ "CX"  "C" "sp3" }
>> 	{ "C8"  "C" "sp3" }
>> 	{ "2C"  "C" "sp3" }
>> 	{ "3C"  "C" "sp3" }
>> 	{ "CH"  "C" "sp3" }
>> 	{ "CS"  "C" "sp2" }
>> 	{ "C"   "C" "sp2" }
>> 	{ "CO"   "C" "sp2" }
>> 	{ "C*"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CB"  "C" "sp2" }
>> 	{ "CC"  "C" "sp2" }
>> 	{ "CN"  "C" "sp2" }
>> 	{ "CM"  "C" "sp2" }
>> 	{ "CK"  "C" "sp2" }
>> 	{ "CQ"  "C" "sp2" }
>> 	{ "CD"  "C" "sp2" }
>> 	{ "C5"  "C" "sp2" }
>> 	{ "C4"  "C" "sp2" }
>> 	{ "CP"  "C" "sp2" }
>> 	{ "CI"  "C" "sp3" }
>> 	{ "CJ"  "C" "sp2" }
>> 	{ "CW"  "C" "sp2" }
>> 	{ "CV"  "C" "sp2" }
>> 	{ "CR"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CY"  "C" "sp2" }
>> 	{ "C0"  "Ca" "sp3" }
>> 	{ "MG"  "Mg" "sp3" }
>> 	{ "N"   "N" "sp2" }
>> 	{ "NA"  "N" "sp2" }
>> 	{ "N2"  "N" "sp2" }
>> 	{ "N*"  "N" "sp2" }
>> 	{ "NP"  "N" "sp2" }
>> 	{ "NQ"  "N" "sp2" }
>> 	{ "NB"  "N" "sp2" }
>> 	{ "NC"  "N" "sp2" }
>> 	{ "NT"  "N" "sp3" }
>> 	{ "NY"  "N" "sp2" }
>> 	{ "N3"  "N" "sp3" }
>> 	{ "S"   "S" "sp3" }
>> 	{ "SH"  "S" "sp3" }
>> 	{ "P"   "P" "sp3" }
>> 	{ "LP"  ""  "sp3" }
>> 	{ "EP"  ""  "sp3" }
>> 	{ "F"   "F" "sp3" }
>> 	{ "Cl"  "Cl" "sp3" }
>> 	{ "Br"  "Br" "sp3" }
>> 	{ "I"   "I"  "sp3" }
>> 	{ "F-"   "F" "sp3" }
>> 	{ "Cl-"  "Cl" "sp3" }
>> 	{ "Br-"  "Br" "sp3" }
>> 	{ "I-"   "I"  "sp3" }
>> 	{ "Li+"  "Li"  "sp3" }
>> 	{ "Na+"  "Na"  "sp3" }
>> 	{ "K+"  "K"  "sp3" }
>> 	{ "Rb+"  "Rb"  "sp3" }
>> 	{ "Cs+"  "Cs"  "sp3" }
>> 	{ "Mg+"  "Mg"  "sp3" }
>> # glycam
>> 	{ "OG"  "O" "sp3" }
>> 	{ "OL"  "O" "sp3" }
>> 	{ "AC"  "C" "sp3" }
>> 	{ "EC"  "C" "sp3" }
>> }
>> #
>> #	Load the main parameter set.
>> #
>> parm10 = loadamberparams parm10.dat
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
(UNKNOWN ATOM TYPE: Zn)
(UNKNOWN ATOM TYPE: EP)
>> frcmod12SB = loadamberparams frcmod.ff12SB
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff12SB
Reading force field modification type file (frcmod)
Reading title:
ff12SB protein backbone and sidechain parameters
>> #
>> #	Load main chain and terminating amino acid libraries, nucleic acids
>> #
>> loadOff amino12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/amino12.lib
Loading: ALA
Loading: ARG
Loading: ASH
Loading: ASN
Loading: ASP
Loading: CYM
Loading: CYS
Loading: CYX
Loading: GLH
Loading: GLN
Loading: GLU
Loading: GLY
Loading: HID
Loading: HIE
Loading: HIP
Loading: HYP
Loading: ILE
Loading: LEU
Loading: LYN
Loading: LYS
Loading: MET
Loading: PHE
Loading: PRO
Loading: SER
Loading: THR
Loading: TRP
Loading: TYR
Loading: VAL
>> loadOff aminoct12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminoct12.lib
Loading: CALA
Loading: CARG
Loading: CASN
Loading: CASP
Loading: CCYS
Loading: CCYX
Loading: CGLN
Loading: CGLU
Loading: CGLY
Loading: CHID
Loading: CHIE
Loading: CHIP
Loading: CHYP
Loading: CILE
Loading: CLEU
Loading: CLYS
Loading: CMET
Loading: CPHE
Loading: CPRO
Loading: CSER
Loading: CTHR
Loading: CTRP
Loading: CTYR
Loading: CVAL
Loading: NHE
Loading: NME
>> loadOff aminont12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminont12.lib
Loading: ACE
Loading: NALA
Loading: NARG
Loading: NASN
Loading: NASP
Loading: NCYS
Loading: NCYX
Loading: NGLN
Loading: NGLU
Loading: NGLY
Loading: NHID
Loading: NHIE
Loading: NHIP
Loading: NILE
Loading: NLEU
Loading: NLYS
Loading: NMET
Loading: NPHE
Loading: NPRO
Loading: NSER
Loading: NTHR
Loading: NTRP
Loading: NTYR
Loading: NVAL
>> loadOff nucleic12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/nucleic12.lib
Loading: A
Loading: A3
Loading: A5
Loading: AN
Loading: C
Loading: C3
Loading: C5
Loading: CN
Loading: DA
Loading: DA3
Loading: DA5
Loading: DAN
Loading: DC
Loading: DC3
Loading: DC5
Loading: DCN
Loading: DG
Loading: DG3
Loading: DG5
Loading: DGN
Loading: DT
Loading: DT3
Loading: DT5
Loading: DTN
Loading: G
Loading: G3
Loading: G5
Loading: GN
Loading: OHE
Loading: U
Loading: U3
Loading: U5
Loading: UN
>> #
>> #       Load water and ions
>> # 
>> loadOff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
>> loadOff solvents.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: MEOHBOX
Loading: NMABOX
Loading: OPC
Loading: OPCBOX
Loading: PL3
Loading: POL3BOX
Loading: QSPCFWBOX
Loading: SPC
Loading: SPCBOX
Loading: SPCFWBOX
Loading: SPF
Loading: SPG
Loading: T4E
Loading: TIP3PBOX
Loading: TIP3PFBOX
Loading: TIP4PBOX
Loading: TIP4PEWBOX
Loading: TIP5PBOX
Loading: TP3
Loading: TP4
Loading: TP5
Loading: TPF
>> HOH = TP3
>> WAT = TP3
>> 
>> #
>> #	Define the PDB name map for the amino acids and nucleic acids
>> #     (note: no NHYP!  use neutral form for now)
>> #
>> addPdbResMap {
>>   { 0 "HYP" "HYP"  } { 1 "HYP" "CHYP" }
>>   { 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
>>   { 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
>>   { 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
>>   { 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
>>   { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
>>   { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
>>   { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
>>   { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
>>   { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
>>   { 0 "HID" "NHID" } { 1 "HID" "CHID" }
>>   { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
>>   { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
>>   { 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
>>   { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
>>   { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
>>   { 0 "MET" "NMET" } { 1 "MET" "CMET" }
>>   { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
>>   { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
>>   { 0 "SER" "NSER" } { 1 "SER" "CSER" }
>>   { 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
>>   { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
>>   { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
>>   { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
>>   { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
>>   { 0 "G" "G5"  } { 1 "G" "G3"  } 
>>   { 0 "A" "A5"  } { 1 "A" "A3"  } 
>>   { 0 "C" "C5"  } { 1 "C" "C3"  } 
>>   { 0 "U" "U5"  } { 1 "U" "U3"  } 
>>   { 0 "DG" "DG5"  } { 1 "DG" "DG3"  }  
>>   { 0 "DA" "DA5"  } { 1 "DA" "DA3"  }  
>>   { 0 "DC" "DC5"  } { 1 "DC" "DC3"  }  
>>   { 0 "DT" "DT5"  } { 1 "DT" "DT3"  }  
>> #  some old Amber residue names for RNA:
>>   { 0  "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" }
>>   { 0  "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" }
>>   { 0  "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" }
>>   { 0  "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" }
>> #  some really old Amber residue names, assuming DNA:
>>   { 0 "GUA" "DG5"  } { 1 "GUA" "DG3"  } { "GUA" "DG" }
>>   { 0 "ADE" "DA5"  } { 1 "ADE" "DA3"  } { "ADE" "DA" }
>>   { 0 "CYT" "DC5"  } { 1 "CYT" "DC3"  } { "CYT" "DC" }
>>   { 0 "THY" "DT5"  } { 1 "THY" "DT3"  } { "THY" "DT" }
>> #  uncomment out the following if you have this old style RNA files:
>> # { 0 "GUA" "G5"  } { 1 "GUA" "G3"  } { "GUA" "G" }
>> # { 0 "ADE" "A5"  } { 1 "ADE" "A3"  } { "ADE" "A" }
>> # { 0 "CYT" "C5"  } { 1 "CYT" "C3"  } { "CYT" "C" }
>> # { 0 "URA" "R5"  } { 1 "URA" "R3"  } { "URA" "R" }
>> 
>> }
>> 
>> #  try to be good about reading in really old atom names as well:
>> addPdbAtomMap {
>>   { "O5*" "O5'" }
>>   { "C5*" "C5'" }
>>   { "C4*" "C4'" }
>>   { "O4*" "O4'" }
>>   { "C3*" "C3'" }
>>   { "O3*" "O3'" }
>>   { "C2*" "C2'" }
>>   { "O2*" "O2'" }
>>   { "C1*" "C1'" }
>>   { "C5M" "C7"  }
>>   { "H1*" "H1'" }
>>   { "H2*1" "H2'" }
>>   { "H2*2" "H2''" }
>>   { "HO*2" "HO2'" }
>>   { "H2'1" "H2'" }
>>   { "H2'2" "H2''" }
>>   { "H3*" "H3'" }
>>   { "H4*" "H4'" }
>>   { "H5*1" "H5'" }
>>   { "H5*2" "H5''" }
>>   { "H5'1" "H5'" }
>>   { "H5'2" "H5''" }
>>   { "HO'2" "HO2'" }
>>   { "H5T"  "HO5'" }
>>   { "H3T"  "HO3'" }
>>   { "O1'" "O4'" }
>>   { "OA"  "OP1" }
>>   { "OB"  "OP2" }
>>   { "O1P" "OP1" }
>>   { "O2P" "OP2" }
>> }
>> 
>> #
>> # assume that most often proteins use HIE
>> #
>> NHIS = NHIE
>> HIS = HIE
>> CHIS = CHIE
> 
> loadoff atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
> loadamberparams frcmod.opc
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.opc
Reading force field modification type file (frcmod)
Reading title:
Parameters for OPC water (JPCL, 2014, 5 (21), pp 3863–3871) 
(UNKNOWN ATOM TYPE: EP)
> loadamberparams frcmod.ionsjc_tip4pew
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip4pew
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP4P/EW water from Joung & Cheatham JPCB (2008)
> 
> m = loadpdb init.pdb
Loading PDB file: ./init.pdb
Enter zPdbReadScan from call depth  0.
Exit  zPdbReadScan from call depth  0.
Matching PDB residue names to LEaP variables.
(Residue 0: A5, Terminal/beginning, was not found in name map.)
(Residue 1: C3, Terminal/last, was not found in name map.)
Joining A5 - C3
  total atoms in file: 63
> 
> 
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.131155 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<H4' 9>
Warning: Close contact of 1.307451 angstroms between .R<C3 2>.A<O3' 31> and .R<C3 2>.A<C4' 8>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> solvatebox m OPCBOX 10.69 iso
  Solute vdw bounding box:              12.265 11.150 10.292
  Total bounding box for atom centers:  33.645 33.645 33.645
      (box expansion for 'iso' is   9.9%)
  Solvent unit box:                     18.865 18.478 19.006
The number of boxes:  x= 2  y= 2  z= 2
Adding box at: x=0  y=0  z=0
Center of solvent box is: 9.432422, 9.239054, 9.503120
Adding box at: x=0  y=0  z=1
Center of solvent box is: 9.432422, 9.239054, -9.503120
Adding box at: x=0  y=1  z=0
Center of solvent box is: 9.432422, -9.239054, 9.503120
Adding box at: x=0  y=1  z=1
Center of solvent box is: 9.432422, -9.239054, -9.503120
Adding box at: x=1  y=0  z=0
Center of solvent box is: -9.432422, 9.239054, 9.503120
Adding box at: x=1  y=0  z=1
Center of solvent box is: -9.432422, 9.239054, -9.503120
Adding box at: x=1  y=1  z=0
Center of solvent box is: -9.432422, -9.239054, 9.503120
Adding box at: x=1  y=1  z=1
Center of solvent box is: -9.432422, -9.239054, -9.503120
  Volume: 48626.484 A^3 
  Total mass 20172.840 amu,  Density 0.689 g/cc
  Added 1088 residues.
> remove m m.1090
> remove m m.1089
> 
> addions m Na+ 0
1 Na+ ion required to neutralize.
Adding 1 counter ions to "m" using 1A grid
Total solute charge:  -1.00  Max atom radius:   2.10
Grid extends from solute vdw + 1.23  to  7.33
Box:
   enclosing:  -11.90 -11.84 -11.12   12.54 11.31 11.09
   sized:			      20.10 20.16 20.88
   edge:        32.00
Resolution:      1.00 Angstrom.
Tree depth: 5
grid build: 0 sec
Volume = 15.67% of box, grid points 5135
Solvent present: replacing closest with ion
	 when steric overlaps occur
Calculating grid charges
charges: 0 sec
(Replacing solvent molecule)
Placed Na+ in m at (-5.98, 4.85, -2.80).

Done adding ions.
> addions m Na+ 5 Cl- 5
Na+ has a charge of 0.
Adding the ions anyway.
Adding 10 counter ions to "m" using 1A grid
Total solute charge:   0.00  Max atom radius:   2.10
Grid extends from solute vdw + 6.14  to  12.24
Box:
   enclosing:  -18.22 -16.75 -16.03   17.46 17.09 16.00
   sized:			      45.78 47.25 47.97
   edge:        64.00
Resolution:      1.00 Angstrom.
Tree depth: 6
grid build: 0 sec
Volume =  4.90% of box, grid points 12839
Solvent present: replacing closest with ion
	 when steric overlaps occur
Calculating grid charges
charges: 0 sec
(Replacing solvent molecule)
Placed Na+ in m at (-0.14, -3.24, 9.75).
(Replacing solvent molecule)
Placed Cl- in m at (2.85, -0.93, 8.58).
(Replacing solvent molecule)
Placed Na+ in m at (8.07, 1.13, 7.86).
(Replacing solvent molecule)
Placed Cl- in m at (-0.46, 0.47, 14.00).
(Replacing solvent molecule)
Placed Na+ in m at (3.98, 1.37, 9.85).
(Replacing solvent molecule)
Placed Cl- in m at (8.42, 0.74, 10.66).
(Replacing solvent molecule)
Placed Na+ in m at (1.80, 4.34, 13.61).
(Replacing solvent molecule)
Placed Cl- in m at (4.87, 5.75, 10.61).
(Replacing solvent molecule)
Placed Na+ in m at (7.00, 4.40, 11.69).
(Replacing solvent molecule)
Placed Cl- in m at (3.61, 1.92, 13.32).

Done adding ions.
> 
> saveamberparm m full.topo non-randomized.crds
Checking Unit.

 -- ignoring the warnings.

Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 ** Warning: No sp2 improper torsion term for  N*-CB-CB-NC
        atoms are: N9 C5 C4 N3
 ** Warning: No sp2 improper torsion term for  NB-CA-CB-CB
        atoms are: N7 C6 C5 C4
 total 11 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
 (no restraints)
> quit
	Quit