log started: Mon May  2 16:41:14 2016

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" }
>>     { "Tl+"  "Tl"  "sp3" }
>>     { "Cu+"  "Cu"  "sp3" }
>>     { "Ag+"  "Ag"  "sp3" }
>>     { "Be2+" "Be"  "sp3" }
>>     { "Cu2+" "Cu"  "sp3" }
>>     { "Ni2+" "Ni"  "sp3" }
>>     { "Pt2+" "Pt"  "sp3" }
>>     { "Zn2+" "Zn"  "sp3" }
>>     { "Co2+" "Co"  "sp3" }
>>     { "Pd2+" "Pd"  "sp3" }
>>     { "Ag2+" "Ag"  "sp3" }
>>     { "Cr2+" "Cr"  "sp3" }
>>     { "Fe2+" "Fe"  "sp3" }
>>     { "Mg2+" "Mg"  "sp3" }
>>     { "V2+"  "V"   "sp3" }
>>     { "Mn2+" "Mn"  "sp3" }
>>     { "Hg2+" "Hg"  "sp3" }
>>     { "Cd2+" "Cd"  "sp3" }
>>     { "Yb2+" "Yb"  "sp3" }
>>     { "Ca2+" "Ca"  "sp3" }
>>     { "Sn2+" "Sn"  "sp3" }
>>     { "Pb2+" "Pb"  "sp3" }
>>     { "Eu2+" "Eu"  "sp3" }
>>     { "Sr2+" "Sr"  "sp3" }
>>     { "Sm2+" "Sm"  "sp3" }
>>     { "Ba2+" "Ba"  "sp3" }
>>     { "Ra2+" "Ra"  "sp3" }
>>     { "Al3+" "Al"  "sp3" }
>>     { "Fe3+" "Fe"  "sp3" }
>>     { "Cr3+" "Cr"  "sp3" }
>>     { "In3+" "In"  "sp3" }
>>     { "Tl3+" "Tl"  "sp3" }
>>     { "Y3+"  "Y"   "sp3" }
>>     { "La3+" "La"  "sp3" }
>>     { "Ce3+" "Ce"  "sp3" }
>>     { "Pr3+" "Pr"  "sp3" }
>>     { "Nd3+" "Nd"  "sp3" }
>>     { "Sm3+" "Sm"  "sp3" }
>>     { "Eu3+" "Eu"  "sp3" }
>>     { "Gd3+" "Gd"  "sp3" }
>>     { "Tb3+" "Tb"  "sp3" }
>>     { "Dy3+" "Dy"  "sp3" }
>>     { "Er3+" "Er"  "sp3" }
>>     { "Tm3+" "Tm"  "sp3" }
>>     { "Lu3+" "Lu"  "sp3" }
>>     { "Hf4+" "Hf"  "sp3" }
>>     { "Zr4+" "Zr"  "sp3" }
>>     { "Ce4+" "Ce"  "sp3" }
>>     { "U4+"  "U"   "sp3" }
>>     { "Pu4+" "Pu"  "sp3" }
>>     { "Th4+" "Th"  "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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: FB3
Loading: FB3BOX
Loading: FB4
Loading: FB4BOX
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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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.ionsjc_tip3p
Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP3P 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: C5, Terminal/beginning, was not found in name map.)
(Residue 1: U3, Terminal/last, was not found in name map.)
Joining C5 - U3
  total atoms in file: 60
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.269303 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<H4' 7>
Warning: Close contact of 1.414096 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<C4' 6>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> 
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.269303 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<H4' 7>
Warning: Close contact of 1.414096 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<C4' 6>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> solvatebox m TIP3PBOX 8 iso
  Solute vdw bounding box:              13.016 10.877 9.893
  Total bounding box for atom centers:  29.016 29.016 29.016
      (box expansion for 'iso' is  21.0%)
  Solvent unit box:                     18.774 18.774 18.774
The number of boxes:  x= 2  y= 2  z= 2
Adding box at: x=0  y=0  z=0
Center of solvent box is: 9.387175, 9.387175, 9.387175
Adding box at: x=0  y=0  z=1
Center of solvent box is: 9.387175, 9.387175, -9.387175
Adding box at: x=0  y=1  z=0
Center of solvent box is: 9.387175, -9.387175, 9.387175
Adding box at: x=0  y=1  z=1
Center of solvent box is: 9.387175, -9.387175, -9.387175
Adding box at: x=1  y=0  z=0
Center of solvent box is: -9.387175, 9.387175, 9.387175
Adding box at: x=1  y=0  z=1
Center of solvent box is: -9.387175, 9.387175, -9.387175
Adding box at: x=1  y=1  z=0
Center of solvent box is: -9.387175, -9.387175, 9.387175
Adding box at: x=1  y=1  z=1
Center of solvent box is: -9.387175, -9.387175, -9.387175
  Volume: 32701.851 A^3 
  Total mass 12727.200 amu,  Density 0.646 g/cc
  Added 676 residues.
> quit
	Quit
log started: Mon May  2 16:41:15 2016

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" }
>>     { "Tl+"  "Tl"  "sp3" }
>>     { "Cu+"  "Cu"  "sp3" }
>>     { "Ag+"  "Ag"  "sp3" }
>>     { "Be2+" "Be"  "sp3" }
>>     { "Cu2+" "Cu"  "sp3" }
>>     { "Ni2+" "Ni"  "sp3" }
>>     { "Pt2+" "Pt"  "sp3" }
>>     { "Zn2+" "Zn"  "sp3" }
>>     { "Co2+" "Co"  "sp3" }
>>     { "Pd2+" "Pd"  "sp3" }
>>     { "Ag2+" "Ag"  "sp3" }
>>     { "Cr2+" "Cr"  "sp3" }
>>     { "Fe2+" "Fe"  "sp3" }
>>     { "Mg2+" "Mg"  "sp3" }
>>     { "V2+"  "V"   "sp3" }
>>     { "Mn2+" "Mn"  "sp3" }
>>     { "Hg2+" "Hg"  "sp3" }
>>     { "Cd2+" "Cd"  "sp3" }
>>     { "Yb2+" "Yb"  "sp3" }
>>     { "Ca2+" "Ca"  "sp3" }
>>     { "Sn2+" "Sn"  "sp3" }
>>     { "Pb2+" "Pb"  "sp3" }
>>     { "Eu2+" "Eu"  "sp3" }
>>     { "Sr2+" "Sr"  "sp3" }
>>     { "Sm2+" "Sm"  "sp3" }
>>     { "Ba2+" "Ba"  "sp3" }
>>     { "Ra2+" "Ra"  "sp3" }
>>     { "Al3+" "Al"  "sp3" }
>>     { "Fe3+" "Fe"  "sp3" }
>>     { "Cr3+" "Cr"  "sp3" }
>>     { "In3+" "In"  "sp3" }
>>     { "Tl3+" "Tl"  "sp3" }
>>     { "Y3+"  "Y"   "sp3" }
>>     { "La3+" "La"  "sp3" }
>>     { "Ce3+" "Ce"  "sp3" }
>>     { "Pr3+" "Pr"  "sp3" }
>>     { "Nd3+" "Nd"  "sp3" }
>>     { "Sm3+" "Sm"  "sp3" }
>>     { "Eu3+" "Eu"  "sp3" }
>>     { "Gd3+" "Gd"  "sp3" }
>>     { "Tb3+" "Tb"  "sp3" }
>>     { "Dy3+" "Dy"  "sp3" }
>>     { "Er3+" "Er"  "sp3" }
>>     { "Tm3+" "Tm"  "sp3" }
>>     { "Lu3+" "Lu"  "sp3" }
>>     { "Hf4+" "Hf"  "sp3" }
>>     { "Zr4+" "Zr"  "sp3" }
>>     { "Ce4+" "Ce"  "sp3" }
>>     { "U4+"  "U"   "sp3" }
>>     { "Pu4+" "Pu"  "sp3" }
>>     { "Th4+" "Th"  "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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: FB3
Loading: FB3BOX
Loading: FB4
Loading: FB4BOX
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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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.ionsjc_tip3p
Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP3P 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: C5, Terminal/beginning, was not found in name map.)
(Residue 1: U3, Terminal/last, was not found in name map.)
Joining C5 - U3
  total atoms in file: 60
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.269303 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<H4' 7>
Warning: Close contact of 1.414096 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<C4' 6>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> 
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.269303 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<H4' 7>
Warning: Close contact of 1.414096 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<C4' 6>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> solvatebox m TIP3PBOX 9 iso
  Solute vdw bounding box:              13.016 10.877 9.893
  Total bounding box for atom centers:  31.016 31.016 31.016
      (box expansion for 'iso' is  19.4%)
  Solvent unit box:                     18.774 18.774 18.774
The number of boxes:  x= 2  y= 2  z= 2
Adding box at: x=0  y=0  z=0
Center of solvent box is: 9.387175, 9.387175, 9.387175
Adding box at: x=0  y=0  z=1
Center of solvent box is: 9.387175, 9.387175, -9.387175
Adding box at: x=0  y=1  z=0
Center of solvent box is: 9.387175, -9.387175, 9.387175
Adding box at: x=0  y=1  z=1
Center of solvent box is: 9.387175, -9.387175, -9.387175
Adding box at: x=1  y=0  z=0
Center of solvent box is: -9.387175, 9.387175, 9.387175
Adding box at: x=1  y=0  z=1
Center of solvent box is: -9.387175, 9.387175, -9.387175
Adding box at: x=1  y=1  z=0
Center of solvent box is: -9.387175, -9.387175, 9.387175
Adding box at: x=1  y=1  z=1
Center of solvent box is: -9.387175, -9.387175, -9.387175
  Volume: 40113.086 A^3 
  Total mass 15519.680 amu,  Density 0.642 g/cc
  Added 831 residues.
> quit
	Quit
log started: Mon May  2 16:41:15 2016

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" }
>>     { "Tl+"  "Tl"  "sp3" }
>>     { "Cu+"  "Cu"  "sp3" }
>>     { "Ag+"  "Ag"  "sp3" }
>>     { "Be2+" "Be"  "sp3" }
>>     { "Cu2+" "Cu"  "sp3" }
>>     { "Ni2+" "Ni"  "sp3" }
>>     { "Pt2+" "Pt"  "sp3" }
>>     { "Zn2+" "Zn"  "sp3" }
>>     { "Co2+" "Co"  "sp3" }
>>     { "Pd2+" "Pd"  "sp3" }
>>     { "Ag2+" "Ag"  "sp3" }
>>     { "Cr2+" "Cr"  "sp3" }
>>     { "Fe2+" "Fe"  "sp3" }
>>     { "Mg2+" "Mg"  "sp3" }
>>     { "V2+"  "V"   "sp3" }
>>     { "Mn2+" "Mn"  "sp3" }
>>     { "Hg2+" "Hg"  "sp3" }
>>     { "Cd2+" "Cd"  "sp3" }
>>     { "Yb2+" "Yb"  "sp3" }
>>     { "Ca2+" "Ca"  "sp3" }
>>     { "Sn2+" "Sn"  "sp3" }
>>     { "Pb2+" "Pb"  "sp3" }
>>     { "Eu2+" "Eu"  "sp3" }
>>     { "Sr2+" "Sr"  "sp3" }
>>     { "Sm2+" "Sm"  "sp3" }
>>     { "Ba2+" "Ba"  "sp3" }
>>     { "Ra2+" "Ra"  "sp3" }
>>     { "Al3+" "Al"  "sp3" }
>>     { "Fe3+" "Fe"  "sp3" }
>>     { "Cr3+" "Cr"  "sp3" }
>>     { "In3+" "In"  "sp3" }
>>     { "Tl3+" "Tl"  "sp3" }
>>     { "Y3+"  "Y"   "sp3" }
>>     { "La3+" "La"  "sp3" }
>>     { "Ce3+" "Ce"  "sp3" }
>>     { "Pr3+" "Pr"  "sp3" }
>>     { "Nd3+" "Nd"  "sp3" }
>>     { "Sm3+" "Sm"  "sp3" }
>>     { "Eu3+" "Eu"  "sp3" }
>>     { "Gd3+" "Gd"  "sp3" }
>>     { "Tb3+" "Tb"  "sp3" }
>>     { "Dy3+" "Dy"  "sp3" }
>>     { "Er3+" "Er"  "sp3" }
>>     { "Tm3+" "Tm"  "sp3" }
>>     { "Lu3+" "Lu"  "sp3" }
>>     { "Hf4+" "Hf"  "sp3" }
>>     { "Zr4+" "Zr"  "sp3" }
>>     { "Ce4+" "Ce"  "sp3" }
>>     { "U4+"  "U"   "sp3" }
>>     { "Pu4+" "Pu"  "sp3" }
>>     { "Th4+" "Th"  "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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: FB3
Loading: FB3BOX
Loading: FB4
Loading: FB4BOX
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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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.ionsjc_tip3p
Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP3P 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: C5, Terminal/beginning, was not found in name map.)
(Residue 1: U3, Terminal/last, was not found in name map.)
Joining C5 - U3
  total atoms in file: 60
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.269303 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<H4' 7>
Warning: Close contact of 1.414096 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<C4' 6>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> 
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.269303 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<H4' 7>
Warning: Close contact of 1.414096 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<C4' 6>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> solvatebox m TIP3PBOX 10 iso
  Solute vdw bounding box:              13.016 10.877 9.893
  Total bounding box for atom centers:  33.016 33.016 33.016
      (box expansion for 'iso' is  18.1%)
  Solvent unit box:                     18.774 18.774 18.774
The number of boxes:  x= 2  y= 2  z= 2
Adding box at: x=0  y=0  z=0
Center of solvent box is: 9.387175, 9.387175, 9.387175
Adding box at: x=0  y=0  z=1
Center of solvent box is: 9.387175, 9.387175, -9.387175
Adding box at: x=0  y=1  z=0
Center of solvent box is: 9.387175, -9.387175, 9.387175
Adding box at: x=0  y=1  z=1
Center of solvent box is: 9.387175, -9.387175, -9.387175
Adding box at: x=1  y=0  z=0
Center of solvent box is: -9.387175, 9.387175, 9.387175
Adding box at: x=1  y=0  z=1
Center of solvent box is: -9.387175, 9.387175, -9.387175
Adding box at: x=1  y=1  z=0
Center of solvent box is: -9.387175, -9.387175, 9.387175
Adding box at: x=1  y=1  z=1
Center of solvent box is: -9.387175, -9.387175, -9.387175
  Volume: 46990.706 A^3 
  Total mass 18654.464 amu,  Density 0.659 g/cc
  Added 1005 residues.
> quit
	Quit
log started: Mon May  2 16:41:15 2016

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" }
>>     { "Tl+"  "Tl"  "sp3" }
>>     { "Cu+"  "Cu"  "sp3" }
>>     { "Ag+"  "Ag"  "sp3" }
>>     { "Be2+" "Be"  "sp3" }
>>     { "Cu2+" "Cu"  "sp3" }
>>     { "Ni2+" "Ni"  "sp3" }
>>     { "Pt2+" "Pt"  "sp3" }
>>     { "Zn2+" "Zn"  "sp3" }
>>     { "Co2+" "Co"  "sp3" }
>>     { "Pd2+" "Pd"  "sp3" }
>>     { "Ag2+" "Ag"  "sp3" }
>>     { "Cr2+" "Cr"  "sp3" }
>>     { "Fe2+" "Fe"  "sp3" }
>>     { "Mg2+" "Mg"  "sp3" }
>>     { "V2+"  "V"   "sp3" }
>>     { "Mn2+" "Mn"  "sp3" }
>>     { "Hg2+" "Hg"  "sp3" }
>>     { "Cd2+" "Cd"  "sp3" }
>>     { "Yb2+" "Yb"  "sp3" }
>>     { "Ca2+" "Ca"  "sp3" }
>>     { "Sn2+" "Sn"  "sp3" }
>>     { "Pb2+" "Pb"  "sp3" }
>>     { "Eu2+" "Eu"  "sp3" }
>>     { "Sr2+" "Sr"  "sp3" }
>>     { "Sm2+" "Sm"  "sp3" }
>>     { "Ba2+" "Ba"  "sp3" }
>>     { "Ra2+" "Ra"  "sp3" }
>>     { "Al3+" "Al"  "sp3" }
>>     { "Fe3+" "Fe"  "sp3" }
>>     { "Cr3+" "Cr"  "sp3" }
>>     { "In3+" "In"  "sp3" }
>>     { "Tl3+" "Tl"  "sp3" }
>>     { "Y3+"  "Y"   "sp3" }
>>     { "La3+" "La"  "sp3" }
>>     { "Ce3+" "Ce"  "sp3" }
>>     { "Pr3+" "Pr"  "sp3" }
>>     { "Nd3+" "Nd"  "sp3" }
>>     { "Sm3+" "Sm"  "sp3" }
>>     { "Eu3+" "Eu"  "sp3" }
>>     { "Gd3+" "Gd"  "sp3" }
>>     { "Tb3+" "Tb"  "sp3" }
>>     { "Dy3+" "Dy"  "sp3" }
>>     { "Er3+" "Er"  "sp3" }
>>     { "Tm3+" "Tm"  "sp3" }
>>     { "Lu3+" "Lu"  "sp3" }
>>     { "Hf4+" "Hf"  "sp3" }
>>     { "Zr4+" "Zr"  "sp3" }
>>     { "Ce4+" "Ce"  "sp3" }
>>     { "U4+"  "U"   "sp3" }
>>     { "Pu4+" "Pu"  "sp3" }
>>     { "Th4+" "Th"  "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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: FB3
Loading: FB3BOX
Loading: FB4
Loading: FB4BOX
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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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.ionsjc_tip3p
Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP3P 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: C5, Terminal/beginning, was not found in name map.)
(Residue 1: U3, Terminal/last, was not found in name map.)
Joining C5 - U3
  total atoms in file: 60
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.269303 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<H4' 7>
Warning: Close contact of 1.414096 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<C4' 6>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> 
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.269303 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<H4' 7>
Warning: Close contact of 1.414096 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<C4' 6>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> solvatebox m TIP3PBOX 11 iso
  Solute vdw bounding box:              13.016 10.877 9.893
  Total bounding box for atom centers:  35.016 35.016 35.016
      (box expansion for 'iso' is  16.9%)
  Solvent unit box:                     18.774 18.774 18.774
The number of boxes:  x= 2  y= 2  z= 2
Adding box at: x=0  y=0  z=0
Center of solvent box is: 9.387175, 9.387175, 9.387175
Adding box at: x=0  y=0  z=1
Center of solvent box is: 9.387175, 9.387175, -9.387175
Adding box at: x=0  y=1  z=0
Center of solvent box is: 9.387175, -9.387175, 9.387175
Adding box at: x=0  y=1  z=1
Center of solvent box is: 9.387175, -9.387175, -9.387175
Adding box at: x=1  y=0  z=0
Center of solvent box is: -9.387175, 9.387175, 9.387175
Adding box at: x=1  y=0  z=1
Center of solvent box is: -9.387175, 9.387175, -9.387175
Adding box at: x=1  y=1  z=0
Center of solvent box is: -9.387175, -9.387175, 9.387175
Adding box at: x=1  y=1  z=1
Center of solvent box is: -9.387175, -9.387175, -9.387175
  Volume: 54358.515 A^3 
  Total mass 22978.304 amu,  Density 0.702 g/cc
  Added 1245 residues.
> quit
	Quit
log started: Mon May  2 16:41:16 2016

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" }
>>     { "Tl+"  "Tl"  "sp3" }
>>     { "Cu+"  "Cu"  "sp3" }
>>     { "Ag+"  "Ag"  "sp3" }
>>     { "Be2+" "Be"  "sp3" }
>>     { "Cu2+" "Cu"  "sp3" }
>>     { "Ni2+" "Ni"  "sp3" }
>>     { "Pt2+" "Pt"  "sp3" }
>>     { "Zn2+" "Zn"  "sp3" }
>>     { "Co2+" "Co"  "sp3" }
>>     { "Pd2+" "Pd"  "sp3" }
>>     { "Ag2+" "Ag"  "sp3" }
>>     { "Cr2+" "Cr"  "sp3" }
>>     { "Fe2+" "Fe"  "sp3" }
>>     { "Mg2+" "Mg"  "sp3" }
>>     { "V2+"  "V"   "sp3" }
>>     { "Mn2+" "Mn"  "sp3" }
>>     { "Hg2+" "Hg"  "sp3" }
>>     { "Cd2+" "Cd"  "sp3" }
>>     { "Yb2+" "Yb"  "sp3" }
>>     { "Ca2+" "Ca"  "sp3" }
>>     { "Sn2+" "Sn"  "sp3" }
>>     { "Pb2+" "Pb"  "sp3" }
>>     { "Eu2+" "Eu"  "sp3" }
>>     { "Sr2+" "Sr"  "sp3" }
>>     { "Sm2+" "Sm"  "sp3" }
>>     { "Ba2+" "Ba"  "sp3" }
>>     { "Ra2+" "Ra"  "sp3" }
>>     { "Al3+" "Al"  "sp3" }
>>     { "Fe3+" "Fe"  "sp3" }
>>     { "Cr3+" "Cr"  "sp3" }
>>     { "In3+" "In"  "sp3" }
>>     { "Tl3+" "Tl"  "sp3" }
>>     { "Y3+"  "Y"   "sp3" }
>>     { "La3+" "La"  "sp3" }
>>     { "Ce3+" "Ce"  "sp3" }
>>     { "Pr3+" "Pr"  "sp3" }
>>     { "Nd3+" "Nd"  "sp3" }
>>     { "Sm3+" "Sm"  "sp3" }
>>     { "Eu3+" "Eu"  "sp3" }
>>     { "Gd3+" "Gd"  "sp3" }
>>     { "Tb3+" "Tb"  "sp3" }
>>     { "Dy3+" "Dy"  "sp3" }
>>     { "Er3+" "Er"  "sp3" }
>>     { "Tm3+" "Tm"  "sp3" }
>>     { "Lu3+" "Lu"  "sp3" }
>>     { "Hf4+" "Hf"  "sp3" }
>>     { "Zr4+" "Zr"  "sp3" }
>>     { "Ce4+" "Ce"  "sp3" }
>>     { "U4+"  "U"   "sp3" }
>>     { "Pu4+" "Pu"  "sp3" }
>>     { "Th4+" "Th"  "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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: FB3
Loading: FB3BOX
Loading: FB4
Loading: FB4BOX
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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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.ionsjc_tip3p
Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP3P 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: C5, Terminal/beginning, was not found in name map.)
(Residue 1: U3, Terminal/last, was not found in name map.)
Joining C5 - U3
  total atoms in file: 60
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.269303 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<H4' 7>
Warning: Close contact of 1.414096 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<C4' 6>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> 
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.269303 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<H4' 7>
Warning: Close contact of 1.414096 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<C4' 6>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> solvatebox m TIP3PBOX 10.5 iso
  Solute vdw bounding box:              13.016 10.877 9.893
  Total bounding box for atom centers:  34.016 34.016 34.016
      (box expansion for 'iso' is  17.5%)
  Solvent unit box:                     18.774 18.774 18.774
The number of boxes:  x= 2  y= 2  z= 2
Adding box at: x=0  y=0  z=0
Center of solvent box is: 9.387175, 9.387175, 9.387175
Adding box at: x=0  y=0  z=1
Center of solvent box is: 9.387175, 9.387175, -9.387175
Adding box at: x=0  y=1  z=0
Center of solvent box is: 9.387175, -9.387175, 9.387175
Adding box at: x=0  y=1  z=1
Center of solvent box is: 9.387175, -9.387175, -9.387175
Adding box at: x=1  y=0  z=0
Center of solvent box is: -9.387175, 9.387175, 9.387175
Adding box at: x=1  y=0  z=1
Center of solvent box is: -9.387175, 9.387175, -9.387175
Adding box at: x=1  y=1  z=0
Center of solvent box is: -9.387175, -9.387175, 9.387175
Adding box at: x=1  y=1  z=1
Center of solvent box is: -9.387175, -9.387175, -9.387175
  Volume: 50773.484 A^3 
  Total mass 20726.304 amu,  Density 0.678 g/cc
  Added 1120 residues.
> quit
	Quit
log started: Mon May  2 16:41:16 2016

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" }
>>     { "Tl+"  "Tl"  "sp3" }
>>     { "Cu+"  "Cu"  "sp3" }
>>     { "Ag+"  "Ag"  "sp3" }
>>     { "Be2+" "Be"  "sp3" }
>>     { "Cu2+" "Cu"  "sp3" }
>>     { "Ni2+" "Ni"  "sp3" }
>>     { "Pt2+" "Pt"  "sp3" }
>>     { "Zn2+" "Zn"  "sp3" }
>>     { "Co2+" "Co"  "sp3" }
>>     { "Pd2+" "Pd"  "sp3" }
>>     { "Ag2+" "Ag"  "sp3" }
>>     { "Cr2+" "Cr"  "sp3" }
>>     { "Fe2+" "Fe"  "sp3" }
>>     { "Mg2+" "Mg"  "sp3" }
>>     { "V2+"  "V"   "sp3" }
>>     { "Mn2+" "Mn"  "sp3" }
>>     { "Hg2+" "Hg"  "sp3" }
>>     { "Cd2+" "Cd"  "sp3" }
>>     { "Yb2+" "Yb"  "sp3" }
>>     { "Ca2+" "Ca"  "sp3" }
>>     { "Sn2+" "Sn"  "sp3" }
>>     { "Pb2+" "Pb"  "sp3" }
>>     { "Eu2+" "Eu"  "sp3" }
>>     { "Sr2+" "Sr"  "sp3" }
>>     { "Sm2+" "Sm"  "sp3" }
>>     { "Ba2+" "Ba"  "sp3" }
>>     { "Ra2+" "Ra"  "sp3" }
>>     { "Al3+" "Al"  "sp3" }
>>     { "Fe3+" "Fe"  "sp3" }
>>     { "Cr3+" "Cr"  "sp3" }
>>     { "In3+" "In"  "sp3" }
>>     { "Tl3+" "Tl"  "sp3" }
>>     { "Y3+"  "Y"   "sp3" }
>>     { "La3+" "La"  "sp3" }
>>     { "Ce3+" "Ce"  "sp3" }
>>     { "Pr3+" "Pr"  "sp3" }
>>     { "Nd3+" "Nd"  "sp3" }
>>     { "Sm3+" "Sm"  "sp3" }
>>     { "Eu3+" "Eu"  "sp3" }
>>     { "Gd3+" "Gd"  "sp3" }
>>     { "Tb3+" "Tb"  "sp3" }
>>     { "Dy3+" "Dy"  "sp3" }
>>     { "Er3+" "Er"  "sp3" }
>>     { "Tm3+" "Tm"  "sp3" }
>>     { "Lu3+" "Lu"  "sp3" }
>>     { "Hf4+" "Hf"  "sp3" }
>>     { "Zr4+" "Zr"  "sp3" }
>>     { "Ce4+" "Ce"  "sp3" }
>>     { "U4+"  "U"   "sp3" }
>>     { "Pu4+" "Pu"  "sp3" }
>>     { "Th4+" "Th"  "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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: FB3
Loading: FB3BOX
Loading: FB4
Loading: FB4BOX
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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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.ionsjc_tip3p
Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP3P 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: C5, Terminal/beginning, was not found in name map.)
(Residue 1: U3, Terminal/last, was not found in name map.)
Joining C5 - U3
  total atoms in file: 60
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.269303 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<H4' 7>
Warning: Close contact of 1.414096 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<C4' 6>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> 
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.269303 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<H4' 7>
Warning: Close contact of 1.414096 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<C4' 6>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> solvatebox m TIP3PBOX 10.4 iso
  Solute vdw bounding box:              13.016 10.877 9.893
  Total bounding box for atom centers:  33.816 33.816 33.816
      (box expansion for 'iso' is  17.6%)
  Solvent unit box:                     18.774 18.774 18.774
The number of boxes:  x= 2  y= 2  z= 2
Adding box at: x=0  y=0  z=0
Center of solvent box is: 9.387175, 9.387175, 9.387175
Adding box at: x=0  y=0  z=1
Center of solvent box is: 9.387175, 9.387175, -9.387175
Adding box at: x=0  y=1  z=0
Center of solvent box is: 9.387175, -9.387175, 9.387175
Adding box at: x=0  y=1  z=1
Center of solvent box is: 9.387175, -9.387175, -9.387175
Adding box at: x=1  y=0  z=0
Center of solvent box is: -9.387175, 9.387175, 9.387175
Adding box at: x=1  y=0  z=1
Center of solvent box is: -9.387175, 9.387175, -9.387175
Adding box at: x=1  y=1  z=0
Center of solvent box is: -9.387175, -9.387175, 9.387175
Adding box at: x=1  y=1  z=1
Center of solvent box is: -9.387175, -9.387175, -9.387175
  Volume: 49828.855 A^3 
  Total mass 20365.984 amu,  Density 0.679 g/cc
  Added 1100 residues.
> quit
	Quit
log started: Mon May  2 16:41:16 2016

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" }
>>     { "Tl+"  "Tl"  "sp3" }
>>     { "Cu+"  "Cu"  "sp3" }
>>     { "Ag+"  "Ag"  "sp3" }
>>     { "Be2+" "Be"  "sp3" }
>>     { "Cu2+" "Cu"  "sp3" }
>>     { "Ni2+" "Ni"  "sp3" }
>>     { "Pt2+" "Pt"  "sp3" }
>>     { "Zn2+" "Zn"  "sp3" }
>>     { "Co2+" "Co"  "sp3" }
>>     { "Pd2+" "Pd"  "sp3" }
>>     { "Ag2+" "Ag"  "sp3" }
>>     { "Cr2+" "Cr"  "sp3" }
>>     { "Fe2+" "Fe"  "sp3" }
>>     { "Mg2+" "Mg"  "sp3" }
>>     { "V2+"  "V"   "sp3" }
>>     { "Mn2+" "Mn"  "sp3" }
>>     { "Hg2+" "Hg"  "sp3" }
>>     { "Cd2+" "Cd"  "sp3" }
>>     { "Yb2+" "Yb"  "sp3" }
>>     { "Ca2+" "Ca"  "sp3" }
>>     { "Sn2+" "Sn"  "sp3" }
>>     { "Pb2+" "Pb"  "sp3" }
>>     { "Eu2+" "Eu"  "sp3" }
>>     { "Sr2+" "Sr"  "sp3" }
>>     { "Sm2+" "Sm"  "sp3" }
>>     { "Ba2+" "Ba"  "sp3" }
>>     { "Ra2+" "Ra"  "sp3" }
>>     { "Al3+" "Al"  "sp3" }
>>     { "Fe3+" "Fe"  "sp3" }
>>     { "Cr3+" "Cr"  "sp3" }
>>     { "In3+" "In"  "sp3" }
>>     { "Tl3+" "Tl"  "sp3" }
>>     { "Y3+"  "Y"   "sp3" }
>>     { "La3+" "La"  "sp3" }
>>     { "Ce3+" "Ce"  "sp3" }
>>     { "Pr3+" "Pr"  "sp3" }
>>     { "Nd3+" "Nd"  "sp3" }
>>     { "Sm3+" "Sm"  "sp3" }
>>     { "Eu3+" "Eu"  "sp3" }
>>     { "Gd3+" "Gd"  "sp3" }
>>     { "Tb3+" "Tb"  "sp3" }
>>     { "Dy3+" "Dy"  "sp3" }
>>     { "Er3+" "Er"  "sp3" }
>>     { "Tm3+" "Tm"  "sp3" }
>>     { "Lu3+" "Lu"  "sp3" }
>>     { "Hf4+" "Hf"  "sp3" }
>>     { "Zr4+" "Zr"  "sp3" }
>>     { "Ce4+" "Ce"  "sp3" }
>>     { "U4+"  "U"   "sp3" }
>>     { "Pu4+" "Pu"  "sp3" }
>>     { "Th4+" "Th"  "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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: FB3
Loading: FB3BOX
Loading: FB4
Loading: FB4BOX
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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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.ionsjc_tip3p
Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP3P 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: C5, Terminal/beginning, was not found in name map.)
(Residue 1: U3, Terminal/last, was not found in name map.)
Joining C5 - U3
  total atoms in file: 60
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.269303 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<H4' 7>
Warning: Close contact of 1.414096 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<C4' 6>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> 
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.269303 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<H4' 7>
Warning: Close contact of 1.414096 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<C4' 6>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> solvatebox m TIP3PBOX 10.3 iso
  Solute vdw bounding box:              13.016 10.877 9.893
  Total bounding box for atom centers:  33.616 33.616 33.616
      (box expansion for 'iso' is  17.7%)
  Solvent unit box:                     18.774 18.774 18.774
The number of boxes:  x= 2  y= 2  z= 2
Adding box at: x=0  y=0  z=0
Center of solvent box is: 9.387175, 9.387175, 9.387175
Adding box at: x=0  y=0  z=1
Center of solvent box is: 9.387175, 9.387175, -9.387175
Adding box at: x=0  y=1  z=0
Center of solvent box is: 9.387175, -9.387175, 9.387175
Adding box at: x=0  y=1  z=1
Center of solvent box is: 9.387175, -9.387175, -9.387175
Adding box at: x=1  y=0  z=0
Center of solvent box is: -9.387175, 9.387175, 9.387175
Adding box at: x=1  y=0  z=1
Center of solvent box is: -9.387175, 9.387175, -9.387175
Adding box at: x=1  y=1  z=0
Center of solvent box is: -9.387175, -9.387175, 9.387175
Adding box at: x=1  y=1  z=1
Center of solvent box is: -9.387175, -9.387175, -9.387175
  Volume: 48794.245 A^3 
  Total mass 19753.440 amu,  Density 0.672 g/cc
  Added 1066 residues.
> quit
	Quit
log started: Mon May  2 16:41:17 2016

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" }
>>     { "Tl+"  "Tl"  "sp3" }
>>     { "Cu+"  "Cu"  "sp3" }
>>     { "Ag+"  "Ag"  "sp3" }
>>     { "Be2+" "Be"  "sp3" }
>>     { "Cu2+" "Cu"  "sp3" }
>>     { "Ni2+" "Ni"  "sp3" }
>>     { "Pt2+" "Pt"  "sp3" }
>>     { "Zn2+" "Zn"  "sp3" }
>>     { "Co2+" "Co"  "sp3" }
>>     { "Pd2+" "Pd"  "sp3" }
>>     { "Ag2+" "Ag"  "sp3" }
>>     { "Cr2+" "Cr"  "sp3" }
>>     { "Fe2+" "Fe"  "sp3" }
>>     { "Mg2+" "Mg"  "sp3" }
>>     { "V2+"  "V"   "sp3" }
>>     { "Mn2+" "Mn"  "sp3" }
>>     { "Hg2+" "Hg"  "sp3" }
>>     { "Cd2+" "Cd"  "sp3" }
>>     { "Yb2+" "Yb"  "sp3" }
>>     { "Ca2+" "Ca"  "sp3" }
>>     { "Sn2+" "Sn"  "sp3" }
>>     { "Pb2+" "Pb"  "sp3" }
>>     { "Eu2+" "Eu"  "sp3" }
>>     { "Sr2+" "Sr"  "sp3" }
>>     { "Sm2+" "Sm"  "sp3" }
>>     { "Ba2+" "Ba"  "sp3" }
>>     { "Ra2+" "Ra"  "sp3" }
>>     { "Al3+" "Al"  "sp3" }
>>     { "Fe3+" "Fe"  "sp3" }
>>     { "Cr3+" "Cr"  "sp3" }
>>     { "In3+" "In"  "sp3" }
>>     { "Tl3+" "Tl"  "sp3" }
>>     { "Y3+"  "Y"   "sp3" }
>>     { "La3+" "La"  "sp3" }
>>     { "Ce3+" "Ce"  "sp3" }
>>     { "Pr3+" "Pr"  "sp3" }
>>     { "Nd3+" "Nd"  "sp3" }
>>     { "Sm3+" "Sm"  "sp3" }
>>     { "Eu3+" "Eu"  "sp3" }
>>     { "Gd3+" "Gd"  "sp3" }
>>     { "Tb3+" "Tb"  "sp3" }
>>     { "Dy3+" "Dy"  "sp3" }
>>     { "Er3+" "Er"  "sp3" }
>>     { "Tm3+" "Tm"  "sp3" }
>>     { "Lu3+" "Lu"  "sp3" }
>>     { "Hf4+" "Hf"  "sp3" }
>>     { "Zr4+" "Zr"  "sp3" }
>>     { "Ce4+" "Ce"  "sp3" }
>>     { "U4+"  "U"   "sp3" }
>>     { "Pu4+" "Pu"  "sp3" }
>>     { "Th4+" "Th"  "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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: FB3
Loading: FB3BOX
Loading: FB4
Loading: FB4BOX
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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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.ionsjc_tip3p
Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP3P 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: C5, Terminal/beginning, was not found in name map.)
(Residue 1: U3, Terminal/last, was not found in name map.)
Joining C5 - U3
  total atoms in file: 60
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.269303 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<H4' 7>
Warning: Close contact of 1.414096 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<C4' 6>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> 
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.269303 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<H4' 7>
Warning: Close contact of 1.414096 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<C4' 6>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> solvatebox m TIP3PBOX 10.35 iso
  Solute vdw bounding box:              13.016 10.877 9.893
  Total bounding box for atom centers:  33.716 33.716 33.716
      (box expansion for 'iso' is  17.7%)
  Solvent unit box:                     18.774 18.774 18.774
The number of boxes:  x= 2  y= 2  z= 2
Adding box at: x=0  y=0  z=0
Center of solvent box is: 9.387175, 9.387175, 9.387175
Adding box at: x=0  y=0  z=1
Center of solvent box is: 9.387175, 9.387175, -9.387175
Adding box at: x=0  y=1  z=0
Center of solvent box is: 9.387175, -9.387175, 9.387175
Adding box at: x=0  y=1  z=1
Center of solvent box is: 9.387175, -9.387175, -9.387175
Adding box at: x=1  y=0  z=0
Center of solvent box is: -9.387175, 9.387175, 9.387175
Adding box at: x=1  y=0  z=1
Center of solvent box is: -9.387175, 9.387175, -9.387175
Adding box at: x=1  y=1  z=0
Center of solvent box is: -9.387175, -9.387175, 9.387175
Adding box at: x=1  y=1  z=1
Center of solvent box is: -9.387175, -9.387175, -9.387175
  Volume: 49828.855 A^3 
  Total mass 20149.792 amu,  Density 0.672 g/cc
  Added 1088 residues.
> quit
	Quit
log started: Mon May  2 16:41:18 2016

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" }
>>     { "Tl+"  "Tl"  "sp3" }
>>     { "Cu+"  "Cu"  "sp3" }
>>     { "Ag+"  "Ag"  "sp3" }
>>     { "Be2+" "Be"  "sp3" }
>>     { "Cu2+" "Cu"  "sp3" }
>>     { "Ni2+" "Ni"  "sp3" }
>>     { "Pt2+" "Pt"  "sp3" }
>>     { "Zn2+" "Zn"  "sp3" }
>>     { "Co2+" "Co"  "sp3" }
>>     { "Pd2+" "Pd"  "sp3" }
>>     { "Ag2+" "Ag"  "sp3" }
>>     { "Cr2+" "Cr"  "sp3" }
>>     { "Fe2+" "Fe"  "sp3" }
>>     { "Mg2+" "Mg"  "sp3" }
>>     { "V2+"  "V"   "sp3" }
>>     { "Mn2+" "Mn"  "sp3" }
>>     { "Hg2+" "Hg"  "sp3" }
>>     { "Cd2+" "Cd"  "sp3" }
>>     { "Yb2+" "Yb"  "sp3" }
>>     { "Ca2+" "Ca"  "sp3" }
>>     { "Sn2+" "Sn"  "sp3" }
>>     { "Pb2+" "Pb"  "sp3" }
>>     { "Eu2+" "Eu"  "sp3" }
>>     { "Sr2+" "Sr"  "sp3" }
>>     { "Sm2+" "Sm"  "sp3" }
>>     { "Ba2+" "Ba"  "sp3" }
>>     { "Ra2+" "Ra"  "sp3" }
>>     { "Al3+" "Al"  "sp3" }
>>     { "Fe3+" "Fe"  "sp3" }
>>     { "Cr3+" "Cr"  "sp3" }
>>     { "In3+" "In"  "sp3" }
>>     { "Tl3+" "Tl"  "sp3" }
>>     { "Y3+"  "Y"   "sp3" }
>>     { "La3+" "La"  "sp3" }
>>     { "Ce3+" "Ce"  "sp3" }
>>     { "Pr3+" "Pr"  "sp3" }
>>     { "Nd3+" "Nd"  "sp3" }
>>     { "Sm3+" "Sm"  "sp3" }
>>     { "Eu3+" "Eu"  "sp3" }
>>     { "Gd3+" "Gd"  "sp3" }
>>     { "Tb3+" "Tb"  "sp3" }
>>     { "Dy3+" "Dy"  "sp3" }
>>     { "Er3+" "Er"  "sp3" }
>>     { "Tm3+" "Tm"  "sp3" }
>>     { "Lu3+" "Lu"  "sp3" }
>>     { "Hf4+" "Hf"  "sp3" }
>>     { "Zr4+" "Zr"  "sp3" }
>>     { "Ce4+" "Ce"  "sp3" }
>>     { "U4+"  "U"   "sp3" }
>>     { "Pu4+" "Pu"  "sp3" }
>>     { "Th4+" "Th"  "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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: FB3
Loading: FB3BOX
Loading: FB4
Loading: FB4BOX
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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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.ionsjc_tip3p
Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP3P 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: C5, Terminal/beginning, was not found in name map.)
(Residue 1: U3, Terminal/last, was not found in name map.)
Joining C5 - U3
  total atoms in file: 60
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.269303 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<H4' 7>
Warning: Close contact of 1.414096 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<C4' 6>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> 
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.269303 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<H4' 7>
Warning: Close contact of 1.414096 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<C4' 6>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> solvateoct m TIP3PBOX 10.35 iso
Scaling up box by a factor of 1.259314 to meet diagonal cut criterion
  Solute vdw bounding box:              13.016 10.877 9.893
  Total bounding box for atom centers:  39.084 39.084 39.084
      (box expansion for 'iso' is  15.0%)
  Solvent unit box:                     18.774 18.774 18.774
The number of boxes:  x= 3  y= 3  z= 3
Adding box at: x=0  y=0  z=0
Center of solvent box is: 18.774349, 18.774349, 18.774349
Adding box at: x=0  y=0  z=1
Center of solvent box is: 18.774349, 18.774349, 0.000000
Adding box at: x=0  y=0  z=2
Center of solvent box is: 18.774349, 18.774349, -18.774349
Adding box at: x=0  y=1  z=0
Center of solvent box is: 18.774349, 0.000000, 18.774349
Adding box at: x=0  y=1  z=1
Center of solvent box is: 18.774349, 0.000000, 0.000000
Adding box at: x=0  y=1  z=2
Center of solvent box is: 18.774349, 0.000000, -18.774349
Adding box at: x=0  y=2  z=0
Center of solvent box is: 18.774349, -18.774349, 18.774349
Adding box at: x=0  y=2  z=1
Center of solvent box is: 18.774349, -18.774349, 0.000000
Adding box at: x=0  y=2  z=2
Center of solvent box is: 18.774349, -18.774349, -18.774349
Adding box at: x=1  y=0  z=0
Center of solvent box is: 0.000000, 18.774349, 18.774349
Adding box at: x=1  y=0  z=1
Center of solvent box is: 0.000000, 18.774349, 0.000000
Adding box at: x=1  y=0  z=2
Center of solvent box is: 0.000000, 18.774349, -18.774349
Adding box at: x=1  y=1  z=0
Center of solvent box is: 0.000000, 0.000000, 18.774349
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, -18.774349
Adding box at: x=1  y=2  z=0
Center of solvent box is: 0.000000, -18.774349, 18.774349
Adding box at: x=1  y=2  z=1
Center of solvent box is: 0.000000, -18.774349, 0.000000
Adding box at: x=1  y=2  z=2
Center of solvent box is: 0.000000, -18.774349, -18.774349
Adding box at: x=2  y=0  z=0
Center of solvent box is: -18.774349, 18.774349, 18.774349
Adding box at: x=2  y=0  z=1
Center of solvent box is: -18.774349, 18.774349, 0.000000
Adding box at: x=2  y=0  z=2
Center of solvent box is: -18.774349, 18.774349, -18.774349
Adding box at: x=2  y=1  z=0
Center of solvent box is: -18.774349, 0.000000, 18.774349
Adding box at: x=2  y=1  z=1
Center of solvent box is: -18.774349, 0.000000, 0.000000
Adding box at: x=2  y=1  z=2
Center of solvent box is: -18.774349, 0.000000, -18.774349
Adding box at: x=2  y=2  z=0
Center of solvent box is: -18.774349, -18.774349, 18.774349
Adding box at: x=2  y=2  z=1
Center of solvent box is: -18.774349, -18.774349, 0.000000
Adding box at: x=2  y=2  z=2
Center of solvent box is: -18.774349, -18.774349, -18.774349
  Volume: 32202.520 A^3 (oct)
  Total mass 16186.272 amu,  Density 0.835 g/cc
  Added 868 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 + 1.37  to  7.47
Box:
   enclosing:  -11.91 -11.65 -12.46   11.19 11.75 10.90
   sized:			      20.09 20.35 19.54
   edge:        32.00
Resolution:      1.00 Angstrom.
Tree depth: 5
grid build: 0 sec
Volume = 15.93% of box, grid points 5220
Solvent present: replacing closest with ion
	 when steric overlaps occur
Calculating grid charges
charges: 0 sec
(Replacing solvent molecule)
Placed Na+ in m at (-4.34, 8.09, 3.45).

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 + 5.59  to  11.69
Box:
   enclosing:  -16.13 -15.87 -16.68   15.41 19.77 15.14
   sized:			      47.87 48.13 47.32
   edge:        64.00
Resolution:      1.00 Angstrom.
Tree depth: 6
grid build: 0 sec
Volume =  4.60% of box, grid points 12063
Solvent present: replacing closest with ion
	 when steric overlaps occur
Calculating grid charges
charges: 0 sec
(Replacing solvent molecule)
Placed Na+ in m at (-10.58, -1.73, -0.86).
(Replacing solvent molecule)
Placed Cl- in m at (-9.52, -2.39, -5.67).
(Replacing solvent molecule)
Placed Na+ in m at (-8.96, -5.32, -8.77).
(Replacing solvent molecule)
Placed Cl- in m at (-9.41, -5.96, -2.48).
(Replacing solvent molecule)
Placed Na+ in m at (-7.02, -8.48, -2.47).
(Replacing solvent molecule)
Placed Cl- in m at (-3.28, -13.13, -6.24).
(Replacing solvent molecule)
Placed Na+ in m at (0.54, -10.88, -6.91).
(Replacing solvent molecule)
Placed Cl- in m at (-3.10, -10.29, -5.97).
(Replacing solvent molecule)
Placed Na+ in m at (-5.58, -10.28, -8.83).
(Replacing solvent molecule)
Placed Cl- in m at (-7.38, -6.44, -11.43).

Done adding ions.
> 
> saveamberparm m full.topo non-randomized.crds
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 12 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
  (Residues lacking connect0/connect1 - 
   these don't have chain types marked:

	res	total affected

	WAT	857
  )
 (no restraints)
> quit
	Quit
log started: Mon May  2 16:41:18 2016

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" }
>>     { "Tl+"  "Tl"  "sp3" }
>>     { "Cu+"  "Cu"  "sp3" }
>>     { "Ag+"  "Ag"  "sp3" }
>>     { "Be2+" "Be"  "sp3" }
>>     { "Cu2+" "Cu"  "sp3" }
>>     { "Ni2+" "Ni"  "sp3" }
>>     { "Pt2+" "Pt"  "sp3" }
>>     { "Zn2+" "Zn"  "sp3" }
>>     { "Co2+" "Co"  "sp3" }
>>     { "Pd2+" "Pd"  "sp3" }
>>     { "Ag2+" "Ag"  "sp3" }
>>     { "Cr2+" "Cr"  "sp3" }
>>     { "Fe2+" "Fe"  "sp3" }
>>     { "Mg2+" "Mg"  "sp3" }
>>     { "V2+"  "V"   "sp3" }
>>     { "Mn2+" "Mn"  "sp3" }
>>     { "Hg2+" "Hg"  "sp3" }
>>     { "Cd2+" "Cd"  "sp3" }
>>     { "Yb2+" "Yb"  "sp3" }
>>     { "Ca2+" "Ca"  "sp3" }
>>     { "Sn2+" "Sn"  "sp3" }
>>     { "Pb2+" "Pb"  "sp3" }
>>     { "Eu2+" "Eu"  "sp3" }
>>     { "Sr2+" "Sr"  "sp3" }
>>     { "Sm2+" "Sm"  "sp3" }
>>     { "Ba2+" "Ba"  "sp3" }
>>     { "Ra2+" "Ra"  "sp3" }
>>     { "Al3+" "Al"  "sp3" }
>>     { "Fe3+" "Fe"  "sp3" }
>>     { "Cr3+" "Cr"  "sp3" }
>>     { "In3+" "In"  "sp3" }
>>     { "Tl3+" "Tl"  "sp3" }
>>     { "Y3+"  "Y"   "sp3" }
>>     { "La3+" "La"  "sp3" }
>>     { "Ce3+" "Ce"  "sp3" }
>>     { "Pr3+" "Pr"  "sp3" }
>>     { "Nd3+" "Nd"  "sp3" }
>>     { "Sm3+" "Sm"  "sp3" }
>>     { "Eu3+" "Eu"  "sp3" }
>>     { "Gd3+" "Gd"  "sp3" }
>>     { "Tb3+" "Tb"  "sp3" }
>>     { "Dy3+" "Dy"  "sp3" }
>>     { "Er3+" "Er"  "sp3" }
>>     { "Tm3+" "Tm"  "sp3" }
>>     { "Lu3+" "Lu"  "sp3" }
>>     { "Hf4+" "Hf"  "sp3" }
>>     { "Zr4+" "Zr"  "sp3" }
>>     { "Ce4+" "Ce"  "sp3" }
>>     { "U4+"  "U"   "sp3" }
>>     { "Pu4+" "Pu"  "sp3" }
>>     { "Th4+" "Th"  "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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: FB3
Loading: FB3BOX
Loading: FB4
Loading: FB4BOX
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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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.ionsjc_tip3p
Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP3P 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: C5, Terminal/beginning, was not found in name map.)
(Residue 1: U3, Terminal/last, was not found in name map.)
Joining C5 - U3
  total atoms in file: 60
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.269303 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<H4' 7>
Warning: Close contact of 1.414096 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<C4' 6>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> 
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.269303 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<H4' 7>
Warning: Close contact of 1.414096 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<C4' 6>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> solvatebox m TIP3PBOX 10.35 iso
  Solute vdw bounding box:              13.016 10.877 9.893
  Total bounding box for atom centers:  33.716 33.716 33.716
      (box expansion for 'iso' is  17.7%)
  Solvent unit box:                     18.774 18.774 18.774
The number of boxes:  x= 2  y= 2  z= 2
Adding box at: x=0  y=0  z=0
Center of solvent box is: 9.387175, 9.387175, 9.387175
Adding box at: x=0  y=0  z=1
Center of solvent box is: 9.387175, 9.387175, -9.387175
Adding box at: x=0  y=1  z=0
Center of solvent box is: 9.387175, -9.387175, 9.387175
Adding box at: x=0  y=1  z=1
Center of solvent box is: 9.387175, -9.387175, -9.387175
Adding box at: x=1  y=0  z=0
Center of solvent box is: -9.387175, 9.387175, 9.387175
Adding box at: x=1  y=0  z=1
Center of solvent box is: -9.387175, 9.387175, -9.387175
Adding box at: x=1  y=1  z=0
Center of solvent box is: -9.387175, -9.387175, 9.387175
Adding box at: x=1  y=1  z=1
Center of solvent box is: -9.387175, -9.387175, -9.387175
  Volume: 49828.855 A^3 
  Total mass 20149.792 amu,  Density 0.672 g/cc
  Added 1088 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 + 1.37  to  7.47
Box:
   enclosing:  -12.52 -11.13 -10.95   12.58 11.75 10.70
   sized:			      19.48 20.87 21.05
   edge:        32.00
Resolution:      1.00 Angstrom.
Tree depth: 5
grid build: 0 sec
Volume = 15.91% of box, grid points 5213
Solvent present: replacing closest with ion
	 when steric overlaps occur
Calculating grid charges
charges: 0 sec
(Replacing solvent molecule)
Placed Na+ in m at (-3.92, 6.17, -3.35).

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 + 5.59  to  11.69
Box:
   enclosing:  -16.74 -15.35 -15.17   16.80 17.86 14.92
   sized:			      47.26 48.65 48.83
   edge:        64.00
Resolution:      1.00 Angstrom.
Tree depth: 6
grid build: 0 sec
Volume =  4.40% of box, grid points 11540
Solvent present: replacing closest with ion
	 when steric overlaps occur
Calculating grid charges
charges: 0 sec
(Replacing solvent molecule)
Placed Na+ in m at (-3.58, 2.24, 9.56).
(Replacing solvent molecule)
Placed Cl- in m at (-6.53, 3.90, 10.56).
(Replacing solvent molecule)
Placed Na+ in m at (-7.99, 6.08, 9.90).
(Replacing solvent molecule)
Placed Cl- in m at (-6.59, 8.82, 7.78).
(Replacing solvent molecule)
Placed Na+ in m at (-3.95, 10.88, 5.53).
(Replacing solvent molecule)
Placed Cl- in m at (-1.12, 10.96, 3.32).
(Replacing solvent molecule)
Placed Na+ in m at (0.79, 12.86, 2.83).
(Replacing solvent molecule)
Placed Cl- in m at (2.37, 12.33, -2.96).
(Replacing solvent molecule)
Placed Na+ in m at (4.78, 10.14, -3.58).
(Replacing solvent molecule)
Placed Cl- in m at (6.29, 11.70, -6.64).

Done adding ions.
> 
> saveamberparm m full.topo non-randomized.crds
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 12 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
  (Residues lacking connect0/connect1 - 
   these don't have chain types marked:

	res	total affected

	WAT	1077
  )
 (no restraints)
> quit
	Quit
log started: Mon May  2 16:41:19 2016

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" }
>>     { "Tl+"  "Tl"  "sp3" }
>>     { "Cu+"  "Cu"  "sp3" }
>>     { "Ag+"  "Ag"  "sp3" }
>>     { "Be2+" "Be"  "sp3" }
>>     { "Cu2+" "Cu"  "sp3" }
>>     { "Ni2+" "Ni"  "sp3" }
>>     { "Pt2+" "Pt"  "sp3" }
>>     { "Zn2+" "Zn"  "sp3" }
>>     { "Co2+" "Co"  "sp3" }
>>     { "Pd2+" "Pd"  "sp3" }
>>     { "Ag2+" "Ag"  "sp3" }
>>     { "Cr2+" "Cr"  "sp3" }
>>     { "Fe2+" "Fe"  "sp3" }
>>     { "Mg2+" "Mg"  "sp3" }
>>     { "V2+"  "V"   "sp3" }
>>     { "Mn2+" "Mn"  "sp3" }
>>     { "Hg2+" "Hg"  "sp3" }
>>     { "Cd2+" "Cd"  "sp3" }
>>     { "Yb2+" "Yb"  "sp3" }
>>     { "Ca2+" "Ca"  "sp3" }
>>     { "Sn2+" "Sn"  "sp3" }
>>     { "Pb2+" "Pb"  "sp3" }
>>     { "Eu2+" "Eu"  "sp3" }
>>     { "Sr2+" "Sr"  "sp3" }
>>     { "Sm2+" "Sm"  "sp3" }
>>     { "Ba2+" "Ba"  "sp3" }
>>     { "Ra2+" "Ra"  "sp3" }
>>     { "Al3+" "Al"  "sp3" }
>>     { "Fe3+" "Fe"  "sp3" }
>>     { "Cr3+" "Cr"  "sp3" }
>>     { "In3+" "In"  "sp3" }
>>     { "Tl3+" "Tl"  "sp3" }
>>     { "Y3+"  "Y"   "sp3" }
>>     { "La3+" "La"  "sp3" }
>>     { "Ce3+" "Ce"  "sp3" }
>>     { "Pr3+" "Pr"  "sp3" }
>>     { "Nd3+" "Nd"  "sp3" }
>>     { "Sm3+" "Sm"  "sp3" }
>>     { "Eu3+" "Eu"  "sp3" }
>>     { "Gd3+" "Gd"  "sp3" }
>>     { "Tb3+" "Tb"  "sp3" }
>>     { "Dy3+" "Dy"  "sp3" }
>>     { "Er3+" "Er"  "sp3" }
>>     { "Tm3+" "Tm"  "sp3" }
>>     { "Lu3+" "Lu"  "sp3" }
>>     { "Hf4+" "Hf"  "sp3" }
>>     { "Zr4+" "Zr"  "sp3" }
>>     { "Ce4+" "Ce"  "sp3" }
>>     { "U4+"  "U"   "sp3" }
>>     { "Pu4+" "Pu"  "sp3" }
>>     { "Th4+" "Th"  "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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: FB3
Loading: FB3BOX
Loading: FB4
Loading: FB4BOX
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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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.ionsjc_tip3p
Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP3P 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: C5, Terminal/beginning, was not found in name map.)
(Residue 1: U3, Terminal/last, was not found in name map.)
Joining C5 - U3
  total atoms in file: 60
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.269303 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<H4' 7>
Warning: Close contact of 1.414096 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<C4' 6>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> 
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.269303 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<H4' 7>
Warning: Close contact of 1.414096 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<C4' 6>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> solvatebox m TIP3PBOX 10.35 iso
  Solute vdw bounding box:              13.016 10.877 9.893
  Total bounding box for atom centers:  33.716 33.716 33.716
      (box expansion for 'iso' is  17.7%)
  Solvent unit box:                     18.774 18.774 18.774
The number of boxes:  x= 2  y= 2  z= 2
Adding box at: x=0  y=0  z=0
Center of solvent box is: 9.387175, 9.387175, 9.387175
Adding box at: x=0  y=0  z=1
Center of solvent box is: 9.387175, 9.387175, -9.387175
Adding box at: x=0  y=1  z=0
Center of solvent box is: 9.387175, -9.387175, 9.387175
Adding box at: x=0  y=1  z=1
Center of solvent box is: 9.387175, -9.387175, -9.387175
Adding box at: x=1  y=0  z=0
Center of solvent box is: -9.387175, 9.387175, 9.387175
Adding box at: x=1  y=0  z=1
Center of solvent box is: -9.387175, 9.387175, -9.387175
Adding box at: x=1  y=1  z=0
Center of solvent box is: -9.387175, -9.387175, 9.387175
Adding box at: x=1  y=1  z=1
Center of solvent box is: -9.387175, -9.387175, -9.387175
  Volume: 49828.855 A^3 
  Total mass 20149.792 amu,  Density 0.672 g/cc
  Added 1088 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 + 1.37  to  7.47
Box:
   enclosing:  -12.52 -11.13 -10.95   12.58 11.75 10.70
   sized:			      19.48 20.87 21.05
   edge:        32.00
Resolution:      1.00 Angstrom.
Tree depth: 5
grid build: 0 sec
Volume = 15.91% of box, grid points 5213
Solvent present: replacing closest with ion
	 when steric overlaps occur
Calculating grid charges
charges: 0 sec
(Replacing solvent molecule)
Placed Na+ in m at (-3.92, 6.17, -3.35).

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 + 5.59  to  11.69
Box:
   enclosing:  -16.74 -15.35 -15.17   16.80 17.86 14.92
   sized:			      47.26 48.65 48.83
   edge:        64.00
Resolution:      1.00 Angstrom.
Tree depth: 6
grid build: 0 sec
Volume =  4.40% of box, grid points 11540
Solvent present: replacing closest with ion
	 when steric overlaps occur
Calculating grid charges
charges: 0 sec
(Replacing solvent molecule)
Placed Na+ in m at (-3.58, 2.24, 9.56).
(Replacing solvent molecule)
Placed Cl- in m at (-6.53, 3.90, 10.56).
(Replacing solvent molecule)
Placed Na+ in m at (-7.99, 6.08, 9.90).
(Replacing solvent molecule)
Placed Cl- in m at (-6.59, 8.82, 7.78).
(Replacing solvent molecule)
Placed Na+ in m at (-3.95, 10.88, 5.53).
(Replacing solvent molecule)
Placed Cl- in m at (-1.12, 10.96, 3.32).
(Replacing solvent molecule)
Placed Na+ in m at (0.79, 12.86, 2.83).
(Replacing solvent molecule)
Placed Cl- in m at (2.37, 12.33, -2.96).
(Replacing solvent molecule)
Placed Na+ in m at (4.78, 10.14, -3.58).
(Replacing solvent molecule)
Placed Cl- in m at (6.29, 11.70, -6.64).

Done adding ions.
> 
> saveamberparm m full.topo non-randomized.crds
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 12 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
  (Residues lacking connect0/connect1 - 
   these don't have chain types marked:

	res	total affected

	WAT	1077
  )
 (no restraints)
> quit
	Quit
log started: Mon May  2 16:41:38 2016

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" }
>>     { "Tl+"  "Tl"  "sp3" }
>>     { "Cu+"  "Cu"  "sp3" }
>>     { "Ag+"  "Ag"  "sp3" }
>>     { "Be2+" "Be"  "sp3" }
>>     { "Cu2+" "Cu"  "sp3" }
>>     { "Ni2+" "Ni"  "sp3" }
>>     { "Pt2+" "Pt"  "sp3" }
>>     { "Zn2+" "Zn"  "sp3" }
>>     { "Co2+" "Co"  "sp3" }
>>     { "Pd2+" "Pd"  "sp3" }
>>     { "Ag2+" "Ag"  "sp3" }
>>     { "Cr2+" "Cr"  "sp3" }
>>     { "Fe2+" "Fe"  "sp3" }
>>     { "Mg2+" "Mg"  "sp3" }
>>     { "V2+"  "V"   "sp3" }
>>     { "Mn2+" "Mn"  "sp3" }
>>     { "Hg2+" "Hg"  "sp3" }
>>     { "Cd2+" "Cd"  "sp3" }
>>     { "Yb2+" "Yb"  "sp3" }
>>     { "Ca2+" "Ca"  "sp3" }
>>     { "Sn2+" "Sn"  "sp3" }
>>     { "Pb2+" "Pb"  "sp3" }
>>     { "Eu2+" "Eu"  "sp3" }
>>     { "Sr2+" "Sr"  "sp3" }
>>     { "Sm2+" "Sm"  "sp3" }
>>     { "Ba2+" "Ba"  "sp3" }
>>     { "Ra2+" "Ra"  "sp3" }
>>     { "Al3+" "Al"  "sp3" }
>>     { "Fe3+" "Fe"  "sp3" }
>>     { "Cr3+" "Cr"  "sp3" }
>>     { "In3+" "In"  "sp3" }
>>     { "Tl3+" "Tl"  "sp3" }
>>     { "Y3+"  "Y"   "sp3" }
>>     { "La3+" "La"  "sp3" }
>>     { "Ce3+" "Ce"  "sp3" }
>>     { "Pr3+" "Pr"  "sp3" }
>>     { "Nd3+" "Nd"  "sp3" }
>>     { "Sm3+" "Sm"  "sp3" }
>>     { "Eu3+" "Eu"  "sp3" }
>>     { "Gd3+" "Gd"  "sp3" }
>>     { "Tb3+" "Tb"  "sp3" }
>>     { "Dy3+" "Dy"  "sp3" }
>>     { "Er3+" "Er"  "sp3" }
>>     { "Tm3+" "Tm"  "sp3" }
>>     { "Lu3+" "Lu"  "sp3" }
>>     { "Hf4+" "Hf"  "sp3" }
>>     { "Zr4+" "Zr"  "sp3" }
>>     { "Ce4+" "Ce"  "sp3" }
>>     { "U4+"  "U"   "sp3" }
>>     { "Pu4+" "Pu"  "sp3" }
>>     { "Th4+" "Th"  "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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: FB3
Loading: FB3BOX
Loading: FB4
Loading: FB4BOX
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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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.ionsjc_tip3p
Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP3P 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: C5, Terminal/beginning, was not found in name map.)
(Residue 1: U3, Terminal/last, was not found in name map.)
Joining C5 - U3
  total atoms in file: 60
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.269303 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<H4' 7>
Warning: Close contact of 1.414096 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<C4' 6>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> 
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.269303 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<H4' 7>
Warning: Close contact of 1.414096 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<C4' 6>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> solvatebox m TIP3PBOX 8 iso
  Solute vdw bounding box:              13.016 10.877 9.893
  Total bounding box for atom centers:  29.016 29.016 29.016
      (box expansion for 'iso' is  21.0%)
  Solvent unit box:                     18.774 18.774 18.774
The number of boxes:  x= 2  y= 2  z= 2
Adding box at: x=0  y=0  z=0
Center of solvent box is: 9.387175, 9.387175, 9.387175
Adding box at: x=0  y=0  z=1
Center of solvent box is: 9.387175, 9.387175, -9.387175
Adding box at: x=0  y=1  z=0
Center of solvent box is: 9.387175, -9.387175, 9.387175
Adding box at: x=0  y=1  z=1
Center of solvent box is: 9.387175, -9.387175, -9.387175
Adding box at: x=1  y=0  z=0
Center of solvent box is: -9.387175, 9.387175, 9.387175
Adding box at: x=1  y=0  z=1
Center of solvent box is: -9.387175, 9.387175, -9.387175
Adding box at: x=1  y=1  z=0
Center of solvent box is: -9.387175, -9.387175, 9.387175
Adding box at: x=1  y=1  z=1
Center of solvent box is: -9.387175, -9.387175, -9.387175
  Volume: 32701.851 A^3 
  Total mass 12727.200 amu,  Density 0.646 g/cc
  Added 676 residues.
> quit
	Quit
log started: Mon May  2 16:41:38 2016

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" }
>>     { "Tl+"  "Tl"  "sp3" }
>>     { "Cu+"  "Cu"  "sp3" }
>>     { "Ag+"  "Ag"  "sp3" }
>>     { "Be2+" "Be"  "sp3" }
>>     { "Cu2+" "Cu"  "sp3" }
>>     { "Ni2+" "Ni"  "sp3" }
>>     { "Pt2+" "Pt"  "sp3" }
>>     { "Zn2+" "Zn"  "sp3" }
>>     { "Co2+" "Co"  "sp3" }
>>     { "Pd2+" "Pd"  "sp3" }
>>     { "Ag2+" "Ag"  "sp3" }
>>     { "Cr2+" "Cr"  "sp3" }
>>     { "Fe2+" "Fe"  "sp3" }
>>     { "Mg2+" "Mg"  "sp3" }
>>     { "V2+"  "V"   "sp3" }
>>     { "Mn2+" "Mn"  "sp3" }
>>     { "Hg2+" "Hg"  "sp3" }
>>     { "Cd2+" "Cd"  "sp3" }
>>     { "Yb2+" "Yb"  "sp3" }
>>     { "Ca2+" "Ca"  "sp3" }
>>     { "Sn2+" "Sn"  "sp3" }
>>     { "Pb2+" "Pb"  "sp3" }
>>     { "Eu2+" "Eu"  "sp3" }
>>     { "Sr2+" "Sr"  "sp3" }
>>     { "Sm2+" "Sm"  "sp3" }
>>     { "Ba2+" "Ba"  "sp3" }
>>     { "Ra2+" "Ra"  "sp3" }
>>     { "Al3+" "Al"  "sp3" }
>>     { "Fe3+" "Fe"  "sp3" }
>>     { "Cr3+" "Cr"  "sp3" }
>>     { "In3+" "In"  "sp3" }
>>     { "Tl3+" "Tl"  "sp3" }
>>     { "Y3+"  "Y"   "sp3" }
>>     { "La3+" "La"  "sp3" }
>>     { "Ce3+" "Ce"  "sp3" }
>>     { "Pr3+" "Pr"  "sp3" }
>>     { "Nd3+" "Nd"  "sp3" }
>>     { "Sm3+" "Sm"  "sp3" }
>>     { "Eu3+" "Eu"  "sp3" }
>>     { "Gd3+" "Gd"  "sp3" }
>>     { "Tb3+" "Tb"  "sp3" }
>>     { "Dy3+" "Dy"  "sp3" }
>>     { "Er3+" "Er"  "sp3" }
>>     { "Tm3+" "Tm"  "sp3" }
>>     { "Lu3+" "Lu"  "sp3" }
>>     { "Hf4+" "Hf"  "sp3" }
>>     { "Zr4+" "Zr"  "sp3" }
>>     { "Ce4+" "Ce"  "sp3" }
>>     { "U4+"  "U"   "sp3" }
>>     { "Pu4+" "Pu"  "sp3" }
>>     { "Th4+" "Th"  "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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: FB3
Loading: FB3BOX
Loading: FB4
Loading: FB4BOX
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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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.ionsjc_tip3p
Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP3P 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: C5, Terminal/beginning, was not found in name map.)
(Residue 1: U3, Terminal/last, was not found in name map.)
Joining C5 - U3
  total atoms in file: 60
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.269303 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<H4' 7>
Warning: Close contact of 1.414096 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<C4' 6>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> 
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.269303 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<H4' 7>
Warning: Close contact of 1.414096 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<C4' 6>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> solvatebox m TIP3PBOX 9 iso
  Solute vdw bounding box:              13.016 10.877 9.893
  Total bounding box for atom centers:  31.016 31.016 31.016
      (box expansion for 'iso' is  19.4%)
  Solvent unit box:                     18.774 18.774 18.774
The number of boxes:  x= 2  y= 2  z= 2
Adding box at: x=0  y=0  z=0
Center of solvent box is: 9.387175, 9.387175, 9.387175
Adding box at: x=0  y=0  z=1
Center of solvent box is: 9.387175, 9.387175, -9.387175
Adding box at: x=0  y=1  z=0
Center of solvent box is: 9.387175, -9.387175, 9.387175
Adding box at: x=0  y=1  z=1
Center of solvent box is: 9.387175, -9.387175, -9.387175
Adding box at: x=1  y=0  z=0
Center of solvent box is: -9.387175, 9.387175, 9.387175
Adding box at: x=1  y=0  z=1
Center of solvent box is: -9.387175, 9.387175, -9.387175
Adding box at: x=1  y=1  z=0
Center of solvent box is: -9.387175, -9.387175, 9.387175
Adding box at: x=1  y=1  z=1
Center of solvent box is: -9.387175, -9.387175, -9.387175
  Volume: 40113.086 A^3 
  Total mass 15519.680 amu,  Density 0.642 g/cc
  Added 831 residues.
> quit
	Quit
log started: Mon May  2 16:41:39 2016

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" }
>>     { "Tl+"  "Tl"  "sp3" }
>>     { "Cu+"  "Cu"  "sp3" }
>>     { "Ag+"  "Ag"  "sp3" }
>>     { "Be2+" "Be"  "sp3" }
>>     { "Cu2+" "Cu"  "sp3" }
>>     { "Ni2+" "Ni"  "sp3" }
>>     { "Pt2+" "Pt"  "sp3" }
>>     { "Zn2+" "Zn"  "sp3" }
>>     { "Co2+" "Co"  "sp3" }
>>     { "Pd2+" "Pd"  "sp3" }
>>     { "Ag2+" "Ag"  "sp3" }
>>     { "Cr2+" "Cr"  "sp3" }
>>     { "Fe2+" "Fe"  "sp3" }
>>     { "Mg2+" "Mg"  "sp3" }
>>     { "V2+"  "V"   "sp3" }
>>     { "Mn2+" "Mn"  "sp3" }
>>     { "Hg2+" "Hg"  "sp3" }
>>     { "Cd2+" "Cd"  "sp3" }
>>     { "Yb2+" "Yb"  "sp3" }
>>     { "Ca2+" "Ca"  "sp3" }
>>     { "Sn2+" "Sn"  "sp3" }
>>     { "Pb2+" "Pb"  "sp3" }
>>     { "Eu2+" "Eu"  "sp3" }
>>     { "Sr2+" "Sr"  "sp3" }
>>     { "Sm2+" "Sm"  "sp3" }
>>     { "Ba2+" "Ba"  "sp3" }
>>     { "Ra2+" "Ra"  "sp3" }
>>     { "Al3+" "Al"  "sp3" }
>>     { "Fe3+" "Fe"  "sp3" }
>>     { "Cr3+" "Cr"  "sp3" }
>>     { "In3+" "In"  "sp3" }
>>     { "Tl3+" "Tl"  "sp3" }
>>     { "Y3+"  "Y"   "sp3" }
>>     { "La3+" "La"  "sp3" }
>>     { "Ce3+" "Ce"  "sp3" }
>>     { "Pr3+" "Pr"  "sp3" }
>>     { "Nd3+" "Nd"  "sp3" }
>>     { "Sm3+" "Sm"  "sp3" }
>>     { "Eu3+" "Eu"  "sp3" }
>>     { "Gd3+" "Gd"  "sp3" }
>>     { "Tb3+" "Tb"  "sp3" }
>>     { "Dy3+" "Dy"  "sp3" }
>>     { "Er3+" "Er"  "sp3" }
>>     { "Tm3+" "Tm"  "sp3" }
>>     { "Lu3+" "Lu"  "sp3" }
>>     { "Hf4+" "Hf"  "sp3" }
>>     { "Zr4+" "Zr"  "sp3" }
>>     { "Ce4+" "Ce"  "sp3" }
>>     { "U4+"  "U"   "sp3" }
>>     { "Pu4+" "Pu"  "sp3" }
>>     { "Th4+" "Th"  "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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: FB3
Loading: FB3BOX
Loading: FB4
Loading: FB4BOX
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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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.ionsjc_tip3p
Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP3P 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: C5, Terminal/beginning, was not found in name map.)
(Residue 1: U3, Terminal/last, was not found in name map.)
Joining C5 - U3
  total atoms in file: 60
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.269303 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<H4' 7>
Warning: Close contact of 1.414096 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<C4' 6>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> 
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.269303 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<H4' 7>
Warning: Close contact of 1.414096 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<C4' 6>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> solvatebox m TIP3PBOX 10 iso
  Solute vdw bounding box:              13.016 10.877 9.893
  Total bounding box for atom centers:  33.016 33.016 33.016
      (box expansion for 'iso' is  18.1%)
  Solvent unit box:                     18.774 18.774 18.774
The number of boxes:  x= 2  y= 2  z= 2
Adding box at: x=0  y=0  z=0
Center of solvent box is: 9.387175, 9.387175, 9.387175
Adding box at: x=0  y=0  z=1
Center of solvent box is: 9.387175, 9.387175, -9.387175
Adding box at: x=0  y=1  z=0
Center of solvent box is: 9.387175, -9.387175, 9.387175
Adding box at: x=0  y=1  z=1
Center of solvent box is: 9.387175, -9.387175, -9.387175
Adding box at: x=1  y=0  z=0
Center of solvent box is: -9.387175, 9.387175, 9.387175
Adding box at: x=1  y=0  z=1
Center of solvent box is: -9.387175, 9.387175, -9.387175
Adding box at: x=1  y=1  z=0
Center of solvent box is: -9.387175, -9.387175, 9.387175
Adding box at: x=1  y=1  z=1
Center of solvent box is: -9.387175, -9.387175, -9.387175
  Volume: 46990.706 A^3 
  Total mass 18654.464 amu,  Density 0.659 g/cc
  Added 1005 residues.
> quit
	Quit
log started: Mon May  2 16:41:39 2016

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" }
>>     { "Tl+"  "Tl"  "sp3" }
>>     { "Cu+"  "Cu"  "sp3" }
>>     { "Ag+"  "Ag"  "sp3" }
>>     { "Be2+" "Be"  "sp3" }
>>     { "Cu2+" "Cu"  "sp3" }
>>     { "Ni2+" "Ni"  "sp3" }
>>     { "Pt2+" "Pt"  "sp3" }
>>     { "Zn2+" "Zn"  "sp3" }
>>     { "Co2+" "Co"  "sp3" }
>>     { "Pd2+" "Pd"  "sp3" }
>>     { "Ag2+" "Ag"  "sp3" }
>>     { "Cr2+" "Cr"  "sp3" }
>>     { "Fe2+" "Fe"  "sp3" }
>>     { "Mg2+" "Mg"  "sp3" }
>>     { "V2+"  "V"   "sp3" }
>>     { "Mn2+" "Mn"  "sp3" }
>>     { "Hg2+" "Hg"  "sp3" }
>>     { "Cd2+" "Cd"  "sp3" }
>>     { "Yb2+" "Yb"  "sp3" }
>>     { "Ca2+" "Ca"  "sp3" }
>>     { "Sn2+" "Sn"  "sp3" }
>>     { "Pb2+" "Pb"  "sp3" }
>>     { "Eu2+" "Eu"  "sp3" }
>>     { "Sr2+" "Sr"  "sp3" }
>>     { "Sm2+" "Sm"  "sp3" }
>>     { "Ba2+" "Ba"  "sp3" }
>>     { "Ra2+" "Ra"  "sp3" }
>>     { "Al3+" "Al"  "sp3" }
>>     { "Fe3+" "Fe"  "sp3" }
>>     { "Cr3+" "Cr"  "sp3" }
>>     { "In3+" "In"  "sp3" }
>>     { "Tl3+" "Tl"  "sp3" }
>>     { "Y3+"  "Y"   "sp3" }
>>     { "La3+" "La"  "sp3" }
>>     { "Ce3+" "Ce"  "sp3" }
>>     { "Pr3+" "Pr"  "sp3" }
>>     { "Nd3+" "Nd"  "sp3" }
>>     { "Sm3+" "Sm"  "sp3" }
>>     { "Eu3+" "Eu"  "sp3" }
>>     { "Gd3+" "Gd"  "sp3" }
>>     { "Tb3+" "Tb"  "sp3" }
>>     { "Dy3+" "Dy"  "sp3" }
>>     { "Er3+" "Er"  "sp3" }
>>     { "Tm3+" "Tm"  "sp3" }
>>     { "Lu3+" "Lu"  "sp3" }
>>     { "Hf4+" "Hf"  "sp3" }
>>     { "Zr4+" "Zr"  "sp3" }
>>     { "Ce4+" "Ce"  "sp3" }
>>     { "U4+"  "U"   "sp3" }
>>     { "Pu4+" "Pu"  "sp3" }
>>     { "Th4+" "Th"  "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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: FB3
Loading: FB3BOX
Loading: FB4
Loading: FB4BOX
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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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.ionsjc_tip3p
Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP3P 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: C5, Terminal/beginning, was not found in name map.)
(Residue 1: U3, Terminal/last, was not found in name map.)
Joining C5 - U3
  total atoms in file: 60
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.269303 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<H4' 7>
Warning: Close contact of 1.414096 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<C4' 6>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> 
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.269303 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<H4' 7>
Warning: Close contact of 1.414096 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<C4' 6>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> solvatebox m TIP3PBOX 11 iso
  Solute vdw bounding box:              13.016 10.877 9.893
  Total bounding box for atom centers:  35.016 35.016 35.016
      (box expansion for 'iso' is  16.9%)
  Solvent unit box:                     18.774 18.774 18.774
The number of boxes:  x= 2  y= 2  z= 2
Adding box at: x=0  y=0  z=0
Center of solvent box is: 9.387175, 9.387175, 9.387175
Adding box at: x=0  y=0  z=1
Center of solvent box is: 9.387175, 9.387175, -9.387175
Adding box at: x=0  y=1  z=0
Center of solvent box is: 9.387175, -9.387175, 9.387175
Adding box at: x=0  y=1  z=1
Center of solvent box is: 9.387175, -9.387175, -9.387175
Adding box at: x=1  y=0  z=0
Center of solvent box is: -9.387175, 9.387175, 9.387175
Adding box at: x=1  y=0  z=1
Center of solvent box is: -9.387175, 9.387175, -9.387175
Adding box at: x=1  y=1  z=0
Center of solvent box is: -9.387175, -9.387175, 9.387175
Adding box at: x=1  y=1  z=1
Center of solvent box is: -9.387175, -9.387175, -9.387175
  Volume: 54358.515 A^3 
  Total mass 22978.304 amu,  Density 0.702 g/cc
  Added 1245 residues.
> quit
	Quit
log started: Mon May  2 16:41:39 2016

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" }
>>     { "Tl+"  "Tl"  "sp3" }
>>     { "Cu+"  "Cu"  "sp3" }
>>     { "Ag+"  "Ag"  "sp3" }
>>     { "Be2+" "Be"  "sp3" }
>>     { "Cu2+" "Cu"  "sp3" }
>>     { "Ni2+" "Ni"  "sp3" }
>>     { "Pt2+" "Pt"  "sp3" }
>>     { "Zn2+" "Zn"  "sp3" }
>>     { "Co2+" "Co"  "sp3" }
>>     { "Pd2+" "Pd"  "sp3" }
>>     { "Ag2+" "Ag"  "sp3" }
>>     { "Cr2+" "Cr"  "sp3" }
>>     { "Fe2+" "Fe"  "sp3" }
>>     { "Mg2+" "Mg"  "sp3" }
>>     { "V2+"  "V"   "sp3" }
>>     { "Mn2+" "Mn"  "sp3" }
>>     { "Hg2+" "Hg"  "sp3" }
>>     { "Cd2+" "Cd"  "sp3" }
>>     { "Yb2+" "Yb"  "sp3" }
>>     { "Ca2+" "Ca"  "sp3" }
>>     { "Sn2+" "Sn"  "sp3" }
>>     { "Pb2+" "Pb"  "sp3" }
>>     { "Eu2+" "Eu"  "sp3" }
>>     { "Sr2+" "Sr"  "sp3" }
>>     { "Sm2+" "Sm"  "sp3" }
>>     { "Ba2+" "Ba"  "sp3" }
>>     { "Ra2+" "Ra"  "sp3" }
>>     { "Al3+" "Al"  "sp3" }
>>     { "Fe3+" "Fe"  "sp3" }
>>     { "Cr3+" "Cr"  "sp3" }
>>     { "In3+" "In"  "sp3" }
>>     { "Tl3+" "Tl"  "sp3" }
>>     { "Y3+"  "Y"   "sp3" }
>>     { "La3+" "La"  "sp3" }
>>     { "Ce3+" "Ce"  "sp3" }
>>     { "Pr3+" "Pr"  "sp3" }
>>     { "Nd3+" "Nd"  "sp3" }
>>     { "Sm3+" "Sm"  "sp3" }
>>     { "Eu3+" "Eu"  "sp3" }
>>     { "Gd3+" "Gd"  "sp3" }
>>     { "Tb3+" "Tb"  "sp3" }
>>     { "Dy3+" "Dy"  "sp3" }
>>     { "Er3+" "Er"  "sp3" }
>>     { "Tm3+" "Tm"  "sp3" }
>>     { "Lu3+" "Lu"  "sp3" }
>>     { "Hf4+" "Hf"  "sp3" }
>>     { "Zr4+" "Zr"  "sp3" }
>>     { "Ce4+" "Ce"  "sp3" }
>>     { "U4+"  "U"   "sp3" }
>>     { "Pu4+" "Pu"  "sp3" }
>>     { "Th4+" "Th"  "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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: FB3
Loading: FB3BOX
Loading: FB4
Loading: FB4BOX
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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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.ionsjc_tip3p
Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP3P 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: C5, Terminal/beginning, was not found in name map.)
(Residue 1: U3, Terminal/last, was not found in name map.)
Joining C5 - U3
  total atoms in file: 60
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.269303 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<H4' 7>
Warning: Close contact of 1.414096 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<C4' 6>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> 
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.269303 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<H4' 7>
Warning: Close contact of 1.414096 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<C4' 6>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> solvatebox m TIP3PBOX 10.5 iso
  Solute vdw bounding box:              13.016 10.877 9.893
  Total bounding box for atom centers:  34.016 34.016 34.016
      (box expansion for 'iso' is  17.5%)
  Solvent unit box:                     18.774 18.774 18.774
The number of boxes:  x= 2  y= 2  z= 2
Adding box at: x=0  y=0  z=0
Center of solvent box is: 9.387175, 9.387175, 9.387175
Adding box at: x=0  y=0  z=1
Center of solvent box is: 9.387175, 9.387175, -9.387175
Adding box at: x=0  y=1  z=0
Center of solvent box is: 9.387175, -9.387175, 9.387175
Adding box at: x=0  y=1  z=1
Center of solvent box is: 9.387175, -9.387175, -9.387175
Adding box at: x=1  y=0  z=0
Center of solvent box is: -9.387175, 9.387175, 9.387175
Adding box at: x=1  y=0  z=1
Center of solvent box is: -9.387175, 9.387175, -9.387175
Adding box at: x=1  y=1  z=0
Center of solvent box is: -9.387175, -9.387175, 9.387175
Adding box at: x=1  y=1  z=1
Center of solvent box is: -9.387175, -9.387175, -9.387175
  Volume: 50773.484 A^3 
  Total mass 20726.304 amu,  Density 0.678 g/cc
  Added 1120 residues.
> quit
	Quit
log started: Mon May  2 16:41:40 2016

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" }
>>     { "Tl+"  "Tl"  "sp3" }
>>     { "Cu+"  "Cu"  "sp3" }
>>     { "Ag+"  "Ag"  "sp3" }
>>     { "Be2+" "Be"  "sp3" }
>>     { "Cu2+" "Cu"  "sp3" }
>>     { "Ni2+" "Ni"  "sp3" }
>>     { "Pt2+" "Pt"  "sp3" }
>>     { "Zn2+" "Zn"  "sp3" }
>>     { "Co2+" "Co"  "sp3" }
>>     { "Pd2+" "Pd"  "sp3" }
>>     { "Ag2+" "Ag"  "sp3" }
>>     { "Cr2+" "Cr"  "sp3" }
>>     { "Fe2+" "Fe"  "sp3" }
>>     { "Mg2+" "Mg"  "sp3" }
>>     { "V2+"  "V"   "sp3" }
>>     { "Mn2+" "Mn"  "sp3" }
>>     { "Hg2+" "Hg"  "sp3" }
>>     { "Cd2+" "Cd"  "sp3" }
>>     { "Yb2+" "Yb"  "sp3" }
>>     { "Ca2+" "Ca"  "sp3" }
>>     { "Sn2+" "Sn"  "sp3" }
>>     { "Pb2+" "Pb"  "sp3" }
>>     { "Eu2+" "Eu"  "sp3" }
>>     { "Sr2+" "Sr"  "sp3" }
>>     { "Sm2+" "Sm"  "sp3" }
>>     { "Ba2+" "Ba"  "sp3" }
>>     { "Ra2+" "Ra"  "sp3" }
>>     { "Al3+" "Al"  "sp3" }
>>     { "Fe3+" "Fe"  "sp3" }
>>     { "Cr3+" "Cr"  "sp3" }
>>     { "In3+" "In"  "sp3" }
>>     { "Tl3+" "Tl"  "sp3" }
>>     { "Y3+"  "Y"   "sp3" }
>>     { "La3+" "La"  "sp3" }
>>     { "Ce3+" "Ce"  "sp3" }
>>     { "Pr3+" "Pr"  "sp3" }
>>     { "Nd3+" "Nd"  "sp3" }
>>     { "Sm3+" "Sm"  "sp3" }
>>     { "Eu3+" "Eu"  "sp3" }
>>     { "Gd3+" "Gd"  "sp3" }
>>     { "Tb3+" "Tb"  "sp3" }
>>     { "Dy3+" "Dy"  "sp3" }
>>     { "Er3+" "Er"  "sp3" }
>>     { "Tm3+" "Tm"  "sp3" }
>>     { "Lu3+" "Lu"  "sp3" }
>>     { "Hf4+" "Hf"  "sp3" }
>>     { "Zr4+" "Zr"  "sp3" }
>>     { "Ce4+" "Ce"  "sp3" }
>>     { "U4+"  "U"   "sp3" }
>>     { "Pu4+" "Pu"  "sp3" }
>>     { "Th4+" "Th"  "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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: FB3
Loading: FB3BOX
Loading: FB4
Loading: FB4BOX
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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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.ionsjc_tip3p
Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP3P 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: C5, Terminal/beginning, was not found in name map.)
(Residue 1: U3, Terminal/last, was not found in name map.)
Joining C5 - U3
  total atoms in file: 60
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.269303 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<H4' 7>
Warning: Close contact of 1.414096 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<C4' 6>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> 
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.269303 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<H4' 7>
Warning: Close contact of 1.414096 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<C4' 6>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> solvatebox m TIP3PBOX 10.4 iso
  Solute vdw bounding box:              13.016 10.877 9.893
  Total bounding box for atom centers:  33.816 33.816 33.816
      (box expansion for 'iso' is  17.6%)
  Solvent unit box:                     18.774 18.774 18.774
The number of boxes:  x= 2  y= 2  z= 2
Adding box at: x=0  y=0  z=0
Center of solvent box is: 9.387175, 9.387175, 9.387175
Adding box at: x=0  y=0  z=1
Center of solvent box is: 9.387175, 9.387175, -9.387175
Adding box at: x=0  y=1  z=0
Center of solvent box is: 9.387175, -9.387175, 9.387175
Adding box at: x=0  y=1  z=1
Center of solvent box is: 9.387175, -9.387175, -9.387175
Adding box at: x=1  y=0  z=0
Center of solvent box is: -9.387175, 9.387175, 9.387175
Adding box at: x=1  y=0  z=1
Center of solvent box is: -9.387175, 9.387175, -9.387175
Adding box at: x=1  y=1  z=0
Center of solvent box is: -9.387175, -9.387175, 9.387175
Adding box at: x=1  y=1  z=1
Center of solvent box is: -9.387175, -9.387175, -9.387175
  Volume: 49828.855 A^3 
  Total mass 20365.984 amu,  Density 0.679 g/cc
  Added 1100 residues.
> quit
	Quit
log started: Mon May  2 16:41:40 2016

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" }
>>     { "Tl+"  "Tl"  "sp3" }
>>     { "Cu+"  "Cu"  "sp3" }
>>     { "Ag+"  "Ag"  "sp3" }
>>     { "Be2+" "Be"  "sp3" }
>>     { "Cu2+" "Cu"  "sp3" }
>>     { "Ni2+" "Ni"  "sp3" }
>>     { "Pt2+" "Pt"  "sp3" }
>>     { "Zn2+" "Zn"  "sp3" }
>>     { "Co2+" "Co"  "sp3" }
>>     { "Pd2+" "Pd"  "sp3" }
>>     { "Ag2+" "Ag"  "sp3" }
>>     { "Cr2+" "Cr"  "sp3" }
>>     { "Fe2+" "Fe"  "sp3" }
>>     { "Mg2+" "Mg"  "sp3" }
>>     { "V2+"  "V"   "sp3" }
>>     { "Mn2+" "Mn"  "sp3" }
>>     { "Hg2+" "Hg"  "sp3" }
>>     { "Cd2+" "Cd"  "sp3" }
>>     { "Yb2+" "Yb"  "sp3" }
>>     { "Ca2+" "Ca"  "sp3" }
>>     { "Sn2+" "Sn"  "sp3" }
>>     { "Pb2+" "Pb"  "sp3" }
>>     { "Eu2+" "Eu"  "sp3" }
>>     { "Sr2+" "Sr"  "sp3" }
>>     { "Sm2+" "Sm"  "sp3" }
>>     { "Ba2+" "Ba"  "sp3" }
>>     { "Ra2+" "Ra"  "sp3" }
>>     { "Al3+" "Al"  "sp3" }
>>     { "Fe3+" "Fe"  "sp3" }
>>     { "Cr3+" "Cr"  "sp3" }
>>     { "In3+" "In"  "sp3" }
>>     { "Tl3+" "Tl"  "sp3" }
>>     { "Y3+"  "Y"   "sp3" }
>>     { "La3+" "La"  "sp3" }
>>     { "Ce3+" "Ce"  "sp3" }
>>     { "Pr3+" "Pr"  "sp3" }
>>     { "Nd3+" "Nd"  "sp3" }
>>     { "Sm3+" "Sm"  "sp3" }
>>     { "Eu3+" "Eu"  "sp3" }
>>     { "Gd3+" "Gd"  "sp3" }
>>     { "Tb3+" "Tb"  "sp3" }
>>     { "Dy3+" "Dy"  "sp3" }
>>     { "Er3+" "Er"  "sp3" }
>>     { "Tm3+" "Tm"  "sp3" }
>>     { "Lu3+" "Lu"  "sp3" }
>>     { "Hf4+" "Hf"  "sp3" }
>>     { "Zr4+" "Zr"  "sp3" }
>>     { "Ce4+" "Ce"  "sp3" }
>>     { "U4+"  "U"   "sp3" }
>>     { "Pu4+" "Pu"  "sp3" }
>>     { "Th4+" "Th"  "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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: FB3
Loading: FB3BOX
Loading: FB4
Loading: FB4BOX
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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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.ionsjc_tip3p
Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP3P 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: C5, Terminal/beginning, was not found in name map.)
(Residue 1: U3, Terminal/last, was not found in name map.)
Joining C5 - U3
  total atoms in file: 60
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.269303 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<H4' 7>
Warning: Close contact of 1.414096 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<C4' 6>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> 
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.269303 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<H4' 7>
Warning: Close contact of 1.414096 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<C4' 6>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> solvatebox m TIP3PBOX 10.3 iso
  Solute vdw bounding box:              13.016 10.877 9.893
  Total bounding box for atom centers:  33.616 33.616 33.616
      (box expansion for 'iso' is  17.7%)
  Solvent unit box:                     18.774 18.774 18.774
The number of boxes:  x= 2  y= 2  z= 2
Adding box at: x=0  y=0  z=0
Center of solvent box is: 9.387175, 9.387175, 9.387175
Adding box at: x=0  y=0  z=1
Center of solvent box is: 9.387175, 9.387175, -9.387175
Adding box at: x=0  y=1  z=0
Center of solvent box is: 9.387175, -9.387175, 9.387175
Adding box at: x=0  y=1  z=1
Center of solvent box is: 9.387175, -9.387175, -9.387175
Adding box at: x=1  y=0  z=0
Center of solvent box is: -9.387175, 9.387175, 9.387175
Adding box at: x=1  y=0  z=1
Center of solvent box is: -9.387175, 9.387175, -9.387175
Adding box at: x=1  y=1  z=0
Center of solvent box is: -9.387175, -9.387175, 9.387175
Adding box at: x=1  y=1  z=1
Center of solvent box is: -9.387175, -9.387175, -9.387175
  Volume: 48794.245 A^3 
  Total mass 19753.440 amu,  Density 0.672 g/cc
  Added 1066 residues.
> quit
	Quit
log started: Mon May  2 16:41:40 2016

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" }
>>     { "Tl+"  "Tl"  "sp3" }
>>     { "Cu+"  "Cu"  "sp3" }
>>     { "Ag+"  "Ag"  "sp3" }
>>     { "Be2+" "Be"  "sp3" }
>>     { "Cu2+" "Cu"  "sp3" }
>>     { "Ni2+" "Ni"  "sp3" }
>>     { "Pt2+" "Pt"  "sp3" }
>>     { "Zn2+" "Zn"  "sp3" }
>>     { "Co2+" "Co"  "sp3" }
>>     { "Pd2+" "Pd"  "sp3" }
>>     { "Ag2+" "Ag"  "sp3" }
>>     { "Cr2+" "Cr"  "sp3" }
>>     { "Fe2+" "Fe"  "sp3" }
>>     { "Mg2+" "Mg"  "sp3" }
>>     { "V2+"  "V"   "sp3" }
>>     { "Mn2+" "Mn"  "sp3" }
>>     { "Hg2+" "Hg"  "sp3" }
>>     { "Cd2+" "Cd"  "sp3" }
>>     { "Yb2+" "Yb"  "sp3" }
>>     { "Ca2+" "Ca"  "sp3" }
>>     { "Sn2+" "Sn"  "sp3" }
>>     { "Pb2+" "Pb"  "sp3" }
>>     { "Eu2+" "Eu"  "sp3" }
>>     { "Sr2+" "Sr"  "sp3" }
>>     { "Sm2+" "Sm"  "sp3" }
>>     { "Ba2+" "Ba"  "sp3" }
>>     { "Ra2+" "Ra"  "sp3" }
>>     { "Al3+" "Al"  "sp3" }
>>     { "Fe3+" "Fe"  "sp3" }
>>     { "Cr3+" "Cr"  "sp3" }
>>     { "In3+" "In"  "sp3" }
>>     { "Tl3+" "Tl"  "sp3" }
>>     { "Y3+"  "Y"   "sp3" }
>>     { "La3+" "La"  "sp3" }
>>     { "Ce3+" "Ce"  "sp3" }
>>     { "Pr3+" "Pr"  "sp3" }
>>     { "Nd3+" "Nd"  "sp3" }
>>     { "Sm3+" "Sm"  "sp3" }
>>     { "Eu3+" "Eu"  "sp3" }
>>     { "Gd3+" "Gd"  "sp3" }
>>     { "Tb3+" "Tb"  "sp3" }
>>     { "Dy3+" "Dy"  "sp3" }
>>     { "Er3+" "Er"  "sp3" }
>>     { "Tm3+" "Tm"  "sp3" }
>>     { "Lu3+" "Lu"  "sp3" }
>>     { "Hf4+" "Hf"  "sp3" }
>>     { "Zr4+" "Zr"  "sp3" }
>>     { "Ce4+" "Ce"  "sp3" }
>>     { "U4+"  "U"   "sp3" }
>>     { "Pu4+" "Pu"  "sp3" }
>>     { "Th4+" "Th"  "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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: FB3
Loading: FB3BOX
Loading: FB4
Loading: FB4BOX
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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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.ionsjc_tip3p
Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP3P 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: C5, Terminal/beginning, was not found in name map.)
(Residue 1: U3, Terminal/last, was not found in name map.)
Joining C5 - U3
  total atoms in file: 60
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.269303 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<H4' 7>
Warning: Close contact of 1.414096 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<C4' 6>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> 
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.269303 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<H4' 7>
Warning: Close contact of 1.414096 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<C4' 6>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> solvatebox m TIP3PBOX 10.35 iso
  Solute vdw bounding box:              13.016 10.877 9.893
  Total bounding box for atom centers:  33.716 33.716 33.716
      (box expansion for 'iso' is  17.7%)
  Solvent unit box:                     18.774 18.774 18.774
The number of boxes:  x= 2  y= 2  z= 2
Adding box at: x=0  y=0  z=0
Center of solvent box is: 9.387175, 9.387175, 9.387175
Adding box at: x=0  y=0  z=1
Center of solvent box is: 9.387175, 9.387175, -9.387175
Adding box at: x=0  y=1  z=0
Center of solvent box is: 9.387175, -9.387175, 9.387175
Adding box at: x=0  y=1  z=1
Center of solvent box is: 9.387175, -9.387175, -9.387175
Adding box at: x=1  y=0  z=0
Center of solvent box is: -9.387175, 9.387175, 9.387175
Adding box at: x=1  y=0  z=1
Center of solvent box is: -9.387175, 9.387175, -9.387175
Adding box at: x=1  y=1  z=0
Center of solvent box is: -9.387175, -9.387175, 9.387175
Adding box at: x=1  y=1  z=1
Center of solvent box is: -9.387175, -9.387175, -9.387175
  Volume: 49828.855 A^3 
  Total mass 20149.792 amu,  Density 0.672 g/cc
  Added 1088 residues.
> quit
	Quit
log started: Mon May  2 16:41:41 2016

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" }
>>     { "Tl+"  "Tl"  "sp3" }
>>     { "Cu+"  "Cu"  "sp3" }
>>     { "Ag+"  "Ag"  "sp3" }
>>     { "Be2+" "Be"  "sp3" }
>>     { "Cu2+" "Cu"  "sp3" }
>>     { "Ni2+" "Ni"  "sp3" }
>>     { "Pt2+" "Pt"  "sp3" }
>>     { "Zn2+" "Zn"  "sp3" }
>>     { "Co2+" "Co"  "sp3" }
>>     { "Pd2+" "Pd"  "sp3" }
>>     { "Ag2+" "Ag"  "sp3" }
>>     { "Cr2+" "Cr"  "sp3" }
>>     { "Fe2+" "Fe"  "sp3" }
>>     { "Mg2+" "Mg"  "sp3" }
>>     { "V2+"  "V"   "sp3" }
>>     { "Mn2+" "Mn"  "sp3" }
>>     { "Hg2+" "Hg"  "sp3" }
>>     { "Cd2+" "Cd"  "sp3" }
>>     { "Yb2+" "Yb"  "sp3" }
>>     { "Ca2+" "Ca"  "sp3" }
>>     { "Sn2+" "Sn"  "sp3" }
>>     { "Pb2+" "Pb"  "sp3" }
>>     { "Eu2+" "Eu"  "sp3" }
>>     { "Sr2+" "Sr"  "sp3" }
>>     { "Sm2+" "Sm"  "sp3" }
>>     { "Ba2+" "Ba"  "sp3" }
>>     { "Ra2+" "Ra"  "sp3" }
>>     { "Al3+" "Al"  "sp3" }
>>     { "Fe3+" "Fe"  "sp3" }
>>     { "Cr3+" "Cr"  "sp3" }
>>     { "In3+" "In"  "sp3" }
>>     { "Tl3+" "Tl"  "sp3" }
>>     { "Y3+"  "Y"   "sp3" }
>>     { "La3+" "La"  "sp3" }
>>     { "Ce3+" "Ce"  "sp3" }
>>     { "Pr3+" "Pr"  "sp3" }
>>     { "Nd3+" "Nd"  "sp3" }
>>     { "Sm3+" "Sm"  "sp3" }
>>     { "Eu3+" "Eu"  "sp3" }
>>     { "Gd3+" "Gd"  "sp3" }
>>     { "Tb3+" "Tb"  "sp3" }
>>     { "Dy3+" "Dy"  "sp3" }
>>     { "Er3+" "Er"  "sp3" }
>>     { "Tm3+" "Tm"  "sp3" }
>>     { "Lu3+" "Lu"  "sp3" }
>>     { "Hf4+" "Hf"  "sp3" }
>>     { "Zr4+" "Zr"  "sp3" }
>>     { "Ce4+" "Ce"  "sp3" }
>>     { "U4+"  "U"   "sp3" }
>>     { "Pu4+" "Pu"  "sp3" }
>>     { "Th4+" "Th"  "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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: FB3
Loading: FB3BOX
Loading: FB4
Loading: FB4BOX
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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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.ionsjc_tip3p
Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP3P 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: C5, Terminal/beginning, was not found in name map.)
(Residue 1: U3, Terminal/last, was not found in name map.)
Joining C5 - U3
  total atoms in file: 60
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.269303 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<H4' 7>
Warning: Close contact of 1.414096 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<C4' 6>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> 
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.269303 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<H4' 7>
Warning: Close contact of 1.414096 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<C4' 6>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> solvateoct m TIP3PBOX 10.35 iso
Scaling up box by a factor of 1.259314 to meet diagonal cut criterion
  Solute vdw bounding box:              13.016 10.877 9.893
  Total bounding box for atom centers:  39.084 39.084 39.084
      (box expansion for 'iso' is  15.0%)
  Solvent unit box:                     18.774 18.774 18.774
The number of boxes:  x= 3  y= 3  z= 3
Adding box at: x=0  y=0  z=0
Center of solvent box is: 18.774349, 18.774349, 18.774349
Adding box at: x=0  y=0  z=1
Center of solvent box is: 18.774349, 18.774349, 0.000000
Adding box at: x=0  y=0  z=2
Center of solvent box is: 18.774349, 18.774349, -18.774349
Adding box at: x=0  y=1  z=0
Center of solvent box is: 18.774349, 0.000000, 18.774349
Adding box at: x=0  y=1  z=1
Center of solvent box is: 18.774349, 0.000000, 0.000000
Adding box at: x=0  y=1  z=2
Center of solvent box is: 18.774349, 0.000000, -18.774349
Adding box at: x=0  y=2  z=0
Center of solvent box is: 18.774349, -18.774349, 18.774349
Adding box at: x=0  y=2  z=1
Center of solvent box is: 18.774349, -18.774349, 0.000000
Adding box at: x=0  y=2  z=2
Center of solvent box is: 18.774349, -18.774349, -18.774349
Adding box at: x=1  y=0  z=0
Center of solvent box is: 0.000000, 18.774349, 18.774349
Adding box at: x=1  y=0  z=1
Center of solvent box is: 0.000000, 18.774349, 0.000000
Adding box at: x=1  y=0  z=2
Center of solvent box is: 0.000000, 18.774349, -18.774349
Adding box at: x=1  y=1  z=0
Center of solvent box is: 0.000000, 0.000000, 18.774349
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, -18.774349
Adding box at: x=1  y=2  z=0
Center of solvent box is: 0.000000, -18.774349, 18.774349
Adding box at: x=1  y=2  z=1
Center of solvent box is: 0.000000, -18.774349, 0.000000
Adding box at: x=1  y=2  z=2
Center of solvent box is: 0.000000, -18.774349, -18.774349
Adding box at: x=2  y=0  z=0
Center of solvent box is: -18.774349, 18.774349, 18.774349
Adding box at: x=2  y=0  z=1
Center of solvent box is: -18.774349, 18.774349, 0.000000
Adding box at: x=2  y=0  z=2
Center of solvent box is: -18.774349, 18.774349, -18.774349
Adding box at: x=2  y=1  z=0
Center of solvent box is: -18.774349, 0.000000, 18.774349
Adding box at: x=2  y=1  z=1
Center of solvent box is: -18.774349, 0.000000, 0.000000
Adding box at: x=2  y=1  z=2
Center of solvent box is: -18.774349, 0.000000, -18.774349
Adding box at: x=2  y=2  z=0
Center of solvent box is: -18.774349, -18.774349, 18.774349
Adding box at: x=2  y=2  z=1
Center of solvent box is: -18.774349, -18.774349, 0.000000
Adding box at: x=2  y=2  z=2
Center of solvent box is: -18.774349, -18.774349, -18.774349
  Volume: 32202.520 A^3 (oct)
  Total mass 16186.272 amu,  Density 0.835 g/cc
  Added 868 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 + 1.37  to  7.47
Box:
   enclosing:  -11.91 -11.65 -12.46   11.19 11.75 10.90
   sized:			      20.09 20.35 19.54
   edge:        32.00
Resolution:      1.00 Angstrom.
Tree depth: 5
grid build: 0 sec
Volume = 15.93% of box, grid points 5220
Solvent present: replacing closest with ion
	 when steric overlaps occur
Calculating grid charges
charges: 0 sec
(Replacing solvent molecule)
Placed Na+ in m at (-4.34, 8.09, 3.45).

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 + 5.59  to  11.69
Box:
   enclosing:  -16.13 -15.87 -16.68   15.41 19.77 15.14
   sized:			      47.87 48.13 47.32
   edge:        64.00
Resolution:      1.00 Angstrom.
Tree depth: 6
grid build: 0 sec
Volume =  4.60% of box, grid points 12063
Solvent present: replacing closest with ion
	 when steric overlaps occur
Calculating grid charges
charges: 0 sec
(Replacing solvent molecule)
Placed Na+ in m at (-10.58, -1.73, -0.86).
(Replacing solvent molecule)
Placed Cl- in m at (-9.52, -2.39, -5.67).
(Replacing solvent molecule)
Placed Na+ in m at (-8.96, -5.32, -8.77).
(Replacing solvent molecule)
Placed Cl- in m at (-9.41, -5.96, -2.48).
(Replacing solvent molecule)
Placed Na+ in m at (-7.02, -8.48, -2.47).
(Replacing solvent molecule)
Placed Cl- in m at (-3.28, -13.13, -6.24).
(Replacing solvent molecule)
Placed Na+ in m at (0.54, -10.88, -6.91).
(Replacing solvent molecule)
Placed Cl- in m at (-3.10, -10.29, -5.97).
(Replacing solvent molecule)
Placed Na+ in m at (-5.58, -10.28, -8.83).
(Replacing solvent molecule)
Placed Cl- in m at (-7.38, -6.44, -11.43).

Done adding ions.
> 
> saveamberparm m full.topo non-randomized.crds
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 12 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
  (Residues lacking connect0/connect1 - 
   these don't have chain types marked:

	res	total affected

	WAT	857
  )
 (no restraints)
> quit
	Quit
log started: Mon May  2 16:41:41 2016

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" }
>>     { "Tl+"  "Tl"  "sp3" }
>>     { "Cu+"  "Cu"  "sp3" }
>>     { "Ag+"  "Ag"  "sp3" }
>>     { "Be2+" "Be"  "sp3" }
>>     { "Cu2+" "Cu"  "sp3" }
>>     { "Ni2+" "Ni"  "sp3" }
>>     { "Pt2+" "Pt"  "sp3" }
>>     { "Zn2+" "Zn"  "sp3" }
>>     { "Co2+" "Co"  "sp3" }
>>     { "Pd2+" "Pd"  "sp3" }
>>     { "Ag2+" "Ag"  "sp3" }
>>     { "Cr2+" "Cr"  "sp3" }
>>     { "Fe2+" "Fe"  "sp3" }
>>     { "Mg2+" "Mg"  "sp3" }
>>     { "V2+"  "V"   "sp3" }
>>     { "Mn2+" "Mn"  "sp3" }
>>     { "Hg2+" "Hg"  "sp3" }
>>     { "Cd2+" "Cd"  "sp3" }
>>     { "Yb2+" "Yb"  "sp3" }
>>     { "Ca2+" "Ca"  "sp3" }
>>     { "Sn2+" "Sn"  "sp3" }
>>     { "Pb2+" "Pb"  "sp3" }
>>     { "Eu2+" "Eu"  "sp3" }
>>     { "Sr2+" "Sr"  "sp3" }
>>     { "Sm2+" "Sm"  "sp3" }
>>     { "Ba2+" "Ba"  "sp3" }
>>     { "Ra2+" "Ra"  "sp3" }
>>     { "Al3+" "Al"  "sp3" }
>>     { "Fe3+" "Fe"  "sp3" }
>>     { "Cr3+" "Cr"  "sp3" }
>>     { "In3+" "In"  "sp3" }
>>     { "Tl3+" "Tl"  "sp3" }
>>     { "Y3+"  "Y"   "sp3" }
>>     { "La3+" "La"  "sp3" }
>>     { "Ce3+" "Ce"  "sp3" }
>>     { "Pr3+" "Pr"  "sp3" }
>>     { "Nd3+" "Nd"  "sp3" }
>>     { "Sm3+" "Sm"  "sp3" }
>>     { "Eu3+" "Eu"  "sp3" }
>>     { "Gd3+" "Gd"  "sp3" }
>>     { "Tb3+" "Tb"  "sp3" }
>>     { "Dy3+" "Dy"  "sp3" }
>>     { "Er3+" "Er"  "sp3" }
>>     { "Tm3+" "Tm"  "sp3" }
>>     { "Lu3+" "Lu"  "sp3" }
>>     { "Hf4+" "Hf"  "sp3" }
>>     { "Zr4+" "Zr"  "sp3" }
>>     { "Ce4+" "Ce"  "sp3" }
>>     { "U4+"  "U"   "sp3" }
>>     { "Pu4+" "Pu"  "sp3" }
>>     { "Th4+" "Th"  "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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: FB3
Loading: FB3BOX
Loading: FB4
Loading: FB4BOX
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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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.ionsjc_tip3p
Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP3P 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: C5, Terminal/beginning, was not found in name map.)
(Residue 1: U3, Terminal/last, was not found in name map.)
Joining C5 - U3
  total atoms in file: 60
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.269303 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<H4' 7>
Warning: Close contact of 1.414096 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<C4' 6>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> 
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.269303 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<H4' 7>
Warning: Close contact of 1.414096 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<C4' 6>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> solvatebox m TIP3PBOX 10.35 iso
  Solute vdw bounding box:              13.016 10.877 9.893
  Total bounding box for atom centers:  33.716 33.716 33.716
      (box expansion for 'iso' is  17.7%)
  Solvent unit box:                     18.774 18.774 18.774
The number of boxes:  x= 2  y= 2  z= 2
Adding box at: x=0  y=0  z=0
Center of solvent box is: 9.387175, 9.387175, 9.387175
Adding box at: x=0  y=0  z=1
Center of solvent box is: 9.387175, 9.387175, -9.387175
Adding box at: x=0  y=1  z=0
Center of solvent box is: 9.387175, -9.387175, 9.387175
Adding box at: x=0  y=1  z=1
Center of solvent box is: 9.387175, -9.387175, -9.387175
Adding box at: x=1  y=0  z=0
Center of solvent box is: -9.387175, 9.387175, 9.387175
Adding box at: x=1  y=0  z=1
Center of solvent box is: -9.387175, 9.387175, -9.387175
Adding box at: x=1  y=1  z=0
Center of solvent box is: -9.387175, -9.387175, 9.387175
Adding box at: x=1  y=1  z=1
Center of solvent box is: -9.387175, -9.387175, -9.387175
  Volume: 49828.855 A^3 
  Total mass 20149.792 amu,  Density 0.672 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 + 1.37  to  7.47
Box:
   enclosing:  -12.52 -11.13 -10.95   12.58 11.75 10.70
   sized:			      19.48 20.87 21.05
   edge:        32.00
Resolution:      1.00 Angstrom.
Tree depth: 5
grid build: 0 sec
Volume = 15.91% of box, grid points 5213
Solvent present: replacing closest with ion
	 when steric overlaps occur
Calculating grid charges
charges: 0 sec
(Replacing solvent molecule)
Placed Na+ in m at (-3.92, 6.17, -3.35).

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 + 5.59  to  11.69
Box:
   enclosing:  -16.74 -15.35 -15.17   16.80 17.86 14.92
   sized:			      47.26 48.65 48.83
   edge:        64.00
Resolution:      1.00 Angstrom.
Tree depth: 6
grid build: 0 sec
Volume =  4.40% of box, grid points 11540
Solvent present: replacing closest with ion
	 when steric overlaps occur
Calculating grid charges
charges: 0 sec
(Replacing solvent molecule)
Placed Na+ in m at (-3.58, 2.24, 9.56).
(Replacing solvent molecule)
Placed Cl- in m at (-6.53, 3.90, 10.56).
(Replacing solvent molecule)
Placed Na+ in m at (-7.99, 6.08, 9.90).
(Replacing solvent molecule)
Placed Cl- in m at (-6.59, 8.82, 7.78).
(Replacing solvent molecule)
Placed Na+ in m at (-3.95, 10.88, 5.53).
(Replacing solvent molecule)
Placed Cl- in m at (-1.12, 10.96, 3.32).
(Replacing solvent molecule)
Placed Na+ in m at (0.79, 12.86, 2.83).
(Replacing solvent molecule)
Placed Cl- in m at (2.37, 12.33, -2.96).
(Replacing solvent molecule)
Placed Na+ in m at (4.78, 10.14, -3.58).
(Replacing solvent molecule)
Placed Cl- in m at (6.29, 11.70, -6.64).

Done adding ions.
> 
> saveamberparm m full.topo non-randomized.crds
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 12 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
  (Residues lacking connect0/connect1 - 
   these don't have chain types marked:

	res	total affected

	WAT	1075
  )
 (no restraints)
> quit
	Quit
log started: Mon May  2 16:41:42 2016

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" }
>>     { "Tl+"  "Tl"  "sp3" }
>>     { "Cu+"  "Cu"  "sp3" }
>>     { "Ag+"  "Ag"  "sp3" }
>>     { "Be2+" "Be"  "sp3" }
>>     { "Cu2+" "Cu"  "sp3" }
>>     { "Ni2+" "Ni"  "sp3" }
>>     { "Pt2+" "Pt"  "sp3" }
>>     { "Zn2+" "Zn"  "sp3" }
>>     { "Co2+" "Co"  "sp3" }
>>     { "Pd2+" "Pd"  "sp3" }
>>     { "Ag2+" "Ag"  "sp3" }
>>     { "Cr2+" "Cr"  "sp3" }
>>     { "Fe2+" "Fe"  "sp3" }
>>     { "Mg2+" "Mg"  "sp3" }
>>     { "V2+"  "V"   "sp3" }
>>     { "Mn2+" "Mn"  "sp3" }
>>     { "Hg2+" "Hg"  "sp3" }
>>     { "Cd2+" "Cd"  "sp3" }
>>     { "Yb2+" "Yb"  "sp3" }
>>     { "Ca2+" "Ca"  "sp3" }
>>     { "Sn2+" "Sn"  "sp3" }
>>     { "Pb2+" "Pb"  "sp3" }
>>     { "Eu2+" "Eu"  "sp3" }
>>     { "Sr2+" "Sr"  "sp3" }
>>     { "Sm2+" "Sm"  "sp3" }
>>     { "Ba2+" "Ba"  "sp3" }
>>     { "Ra2+" "Ra"  "sp3" }
>>     { "Al3+" "Al"  "sp3" }
>>     { "Fe3+" "Fe"  "sp3" }
>>     { "Cr3+" "Cr"  "sp3" }
>>     { "In3+" "In"  "sp3" }
>>     { "Tl3+" "Tl"  "sp3" }
>>     { "Y3+"  "Y"   "sp3" }
>>     { "La3+" "La"  "sp3" }
>>     { "Ce3+" "Ce"  "sp3" }
>>     { "Pr3+" "Pr"  "sp3" }
>>     { "Nd3+" "Nd"  "sp3" }
>>     { "Sm3+" "Sm"  "sp3" }
>>     { "Eu3+" "Eu"  "sp3" }
>>     { "Gd3+" "Gd"  "sp3" }
>>     { "Tb3+" "Tb"  "sp3" }
>>     { "Dy3+" "Dy"  "sp3" }
>>     { "Er3+" "Er"  "sp3" }
>>     { "Tm3+" "Tm"  "sp3" }
>>     { "Lu3+" "Lu"  "sp3" }
>>     { "Hf4+" "Hf"  "sp3" }
>>     { "Zr4+" "Zr"  "sp3" }
>>     { "Ce4+" "Ce"  "sp3" }
>>     { "U4+"  "U"   "sp3" }
>>     { "Pu4+" "Pu"  "sp3" }
>>     { "Th4+" "Th"  "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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: FB3
Loading: FB3BOX
Loading: FB4
Loading: FB4BOX
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: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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.ionsjc_tip3p
Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP3P 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: C5, Terminal/beginning, was not found in name map.)
(Residue 1: U3, Terminal/last, was not found in name map.)
Joining C5 - U3
  total atoms in file: 60
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.269303 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<H4' 7>
Warning: Close contact of 1.414096 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<C4' 6>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> 
> 
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.269303 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<H4' 7>
Warning: Close contact of 1.414096 angstroms between .R<C5 1>.A<O3' 29> and .R<C5 1>.A<C4' 6>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
> 
> solvatebox m TIP3PBOX 10.35 iso
  Solute vdw bounding box:              13.016 10.877 9.893
  Total bounding box for atom centers:  33.716 33.716 33.716
      (box expansion for 'iso' is  17.7%)
  Solvent unit box:                     18.774 18.774 18.774
The number of boxes:  x= 2  y= 2  z= 2
Adding box at: x=0  y=0  z=0
Center of solvent box is: 9.387175, 9.387175, 9.387175
Adding box at: x=0  y=0  z=1
Center of solvent box is: 9.387175, 9.387175, -9.387175
Adding box at: x=0  y=1  z=0
Center of solvent box is: 9.387175, -9.387175, 9.387175
Adding box at: x=0  y=1  z=1
Center of solvent box is: 9.387175, -9.387175, -9.387175
Adding box at: x=1  y=0  z=0
Center of solvent box is: -9.387175, 9.387175, 9.387175
Adding box at: x=1  y=0  z=1
Center of solvent box is: -9.387175, 9.387175, -9.387175
Adding box at: x=1  y=1  z=0
Center of solvent box is: -9.387175, -9.387175, 9.387175
Adding box at: x=1  y=1  z=1
Center of solvent box is: -9.387175, -9.387175, -9.387175
  Volume: 49828.855 A^3 
  Total mass 20149.792 amu,  Density 0.672 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 + 1.37  to  7.47
Box:
   enclosing:  -12.52 -11.13 -10.95   12.58 11.75 10.70
   sized:			      19.48 20.87 21.05
   edge:        32.00
Resolution:      1.00 Angstrom.
Tree depth: 5
grid build: 0 sec
Volume = 15.91% of box, grid points 5213
Solvent present: replacing closest with ion
	 when steric overlaps occur
Calculating grid charges
charges: 0 sec
(Replacing solvent molecule)
Placed Na+ in m at (-3.92, 6.17, -3.35).

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 + 5.59  to  11.69
Box:
   enclosing:  -16.74 -15.35 -15.17   16.80 17.86 14.92
   sized:			      47.26 48.65 48.83
   edge:        64.00
Resolution:      1.00 Angstrom.
Tree depth: 6
grid build: 0 sec
Volume =  4.40% of box, grid points 11540
Solvent present: replacing closest with ion
	 when steric overlaps occur
Calculating grid charges
charges: 0 sec
(Replacing solvent molecule)
Placed Na+ in m at (-3.58, 2.24, 9.56).
(Replacing solvent molecule)
Placed Cl- in m at (-6.53, 3.90, 10.56).
(Replacing solvent molecule)
Placed Na+ in m at (-7.99, 6.08, 9.90).
(Replacing solvent molecule)
Placed Cl- in m at (-6.59, 8.82, 7.78).
(Replacing solvent molecule)
Placed Na+ in m at (-3.95, 10.88, 5.53).
(Replacing solvent molecule)
Placed Cl- in m at (-1.12, 10.96, 3.32).
(Replacing solvent molecule)
Placed Na+ in m at (0.79, 12.86, 2.83).
(Replacing solvent molecule)
Placed Cl- in m at (2.37, 12.33, -2.96).
(Replacing solvent molecule)
Placed Na+ in m at (4.78, 10.14, -3.58).
(Replacing solvent molecule)
Placed Cl- in m at (6.29, 11.70, -6.64).

Done adding ions.
> 
> saveamberparm m full.topo non-randomized.crds
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 12 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
  (Residues lacking connect0/connect1 - 
   these don't have chain types marked:

	res	total affected

	WAT	1075
  )
 (no restraints)
> quit
	Quit