log started: Fri Aug 15 12:56:14 2008

Log file: ./leap.log
> #
> # ----- leaprc for loading the ff99SB (Hornak & Simmerling) force field
> #
> #	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" }
> 	{ "OH"  "O" "sp3" }
> 	{ "OS"  "O" "sp3" }
> 	{ "O"   "O" "sp2" }
> 	{ "O2"  "O" "sp2" }
> 	{ "OW"  "O" "sp3" }
> 	{ "CT"  "C" "sp3" }
> 	{ "CH"  "C" "sp3" }
> 	{ "C2"  "C" "sp3" }
> 	{ "C3"  "C" "sp3" }
> 	{ "C"   "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" }
> 	{ "CE"  "C" "sp2" }
> 	{ "CF"  "C" "sp2" }
> 	{ "CG"  "C" "sp2" }
> 	{ "CP"  "C" "sp2" }
> 	{ "CI"  "C" "sp2" }
> 	{ "CJ"  "C" "sp2" }
> 	{ "CW"  "C" "sp2" }
> 	{ "CV"  "C" "sp2" }
> 	{ "CR"  "C" "sp2" }
> 	{ "CA"  "C" "sp2" }
> 	{ "CY"  "C" "sp2" }
> 	{ "C0"  "C" "sp2" }
> 	{ "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" }
> 	{ "N3"  "N" "sp3" }
> 	{ "S"   "S" "sp3" }
> 	{ "SH"  "S" "sp3" }
> 	{ "P"   "P" "sp3" }
> 	{ "LP"  ""  "sp3" }
> 	{ "F"   "F" "sp3" }
> 	{ "CL"  "Cl" "sp3" }
> 	{ "BR"  "Br" "sp3" }
> 	{ "I"   "I"  "sp3" }
> 	{ "FE"  "Fe" "sp3" }
> 	{ "EP"  ""  "sp3" }
> # glycam
> 	{ "OG"  "O" "sp3" }
> 	{ "OL"  "O" "sp3" }
> 	{ "AC"  "C" "sp3" }
> 	{ "EC"  "C" "sp3" }
> }
> #
> #	Load the main parameter set.
> #
> parm99 = loadamberparams parm99.dat
Loading parameters: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/parm/parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99
(UNKNOWN ATOM TYPE: HZ)
(UNKNOWN ATOM TYPE: NY)
(UNKNOWN ATOM TYPE: IM)
(UNKNOWN ATOM TYPE: Li)
(UNKNOWN ATOM TYPE: IP)
(UNKNOWN ATOM TYPE: K)
(UNKNOWN ATOM TYPE: Rb)
(UNKNOWN ATOM TYPE: Cs)
(UNKNOWN ATOM TYPE: Zn)
(UNKNOWN ATOM TYPE: IB)
(UNKNOWN ATOM TYPE: LP)
> frcmod99SB = loadamberparams frcmod.ff99SB
Loading parameters: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/parm/frcmod.ff99SB
Reading force field modification type file (frcmod)
Reading title:
Modification/update of parm99.dat (Hornak & Simmerling)
> #
> #	Load DNA/RNA libraries
> #
> loadOff all_nucleic94.lib
Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/all_nucleic94.lib
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: RA
Loading: RA3
Loading: RA5
Loading: RAN
Loading: RC
Loading: RC3
Loading: RC5
Loading: RCN
Loading: RG
Loading: RG3
Loading: RG5
Loading: RGN
Loading: RU
Loading: RU3
Loading: RU5
Loading: RUN
> #
> #	Load main chain and terminating 
> #	amino acid libraries (i.e. ff94 libs)
> #
> loadOff all_amino94.lib
Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/all_amino94.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: ILE
Loading: LEU
Loading: LYN
Loading: LYS
Loading: MET
Loading: PHE
Loading: PRO
Loading: SER
Loading: THR
Loading: TRP
Loading: TYR
Loading: VAL
> loadOff all_aminoct94.lib
Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/all_aminoct94.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: 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 all_aminont94.lib
Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/all_aminont94.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
> #
> #       Load water and ions
> # 
> loadOff ions94.lib
Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/ions94.lib
Loading: CIO
Loading: Cl-
Loading: Cs+
Loading: IB
Loading: K+
Loading: Li+
Loading: MG2
Loading: Na+
Loading: Rb+
> loadOff solvents.lib
Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: MEOHBOX
Loading: NMABOX
Loading: PL3
Loading: POL3BOX
Loading: SPC
Loading: SPCBOX
Loading: SPCFWBOX
Loading: SPF
Loading: T4E
Loading: TIP3PBOX
Loading: TIP4PBOX
Loading: TIP4PEWBOX
Loading: TP3
Loading: TP4
Loading: TP5
> HOH = TP3
> WAT = TP3
> 
> #
> #	Define the PDB name map for the amino acids and DNA.
> #
> addPdbResMap {
>   { 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 "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" }
>   { 0 "G" "DG5"  } { 1 "G" "DG3"  } { "G" "DG" } { "GN" "DGN" }
>   { 0 "A" "DA5"  } { 1 "A" "DA3"  } { "A" "DA" } { "AN" "DAN" }
>   { 0 "C" "DC5"  } { 1 "C" "DC3"  } { "C" "DC" } { "CN" "DCN" }
>   { 0 "T" "DT5"  } { 1 "T" "DT3"  } { "T" "DT" } { "TN" "DTN" }
>   { 0 "C5" "DC5" }
>   { 0 "G5" "DG5" }
>   { 0 "A5" "DA5" }
>   { 0 "T5" "DT5" }
>   { 1 "C3" "DC3" }
>   { 1 "G3" "DG3" }
>   { 1 "A3" "DA3" }
>   { 1 "T3" "DT3" }
> 
> }
> 
> addPdbAtomMap {
>   { "O5*" "O5'" }
>   { "C5*" "C5'" }
>   { "C4*" "C4'" }
>   { "O4*" "O4'" }
>   { "C3*" "C3'" }
>   { "O3*" "O3'" }
>   { "C2*" "C2'" }
>   { "C1*" "C1'" }
>   { "C5M" "C7"  }
>   { "H1*" "H1'" }
>   { "H2*1" "H2'1" }
>   { "H2*2" "H2'2" }
>   { "H3*" "H3'" }
>   { "H4*" "H4'" }
>   { "H5*1" "H5'1" }
>   { "H5*2" "H5'2" }
> # old ff atom names -> new
>   { "O1'" "O4'" }
>   { "OA"  "O1P" }
>   { "OB"  "O2P" }
> }
> 
> 
> #
> # assumed that most often proteins use HIE
> #
> NHIS = NHIE
> HIS = HIE
> CHIS = CHIE
 
Sourcing: ./buildit
> 
> #CM5 = loadmol2 cm5.mol2
> #TMI = loadmol2 tmi.mol2
> loadoff heme.off
Loading library: ./heme.off
Loading: HEM
> gaff = loadamberparams gaff.dat
Loading parameters: ./gaff.dat
Reading title:
AMBER General Force Field for organic mol., add. info. at the end (June, 2003)
(UNKNOWN ATOM TYPE: hn)
(UNKNOWN ATOM TYPE: hx)
(UNKNOWN ATOM TYPE: c1)
(UNKNOWN ATOM TYPE: cu)
(UNKNOWN ATOM TYPE: cx)
(UNKNOWN ATOM TYPE: n1)
(UNKNOWN ATOM TYPE: n4)
(UNKNOWN ATOM TYPE: nd)
(UNKNOWN ATOM TYPE: ne)
(UNKNOWN ATOM TYPE: nf)
(UNKNOWN ATOM TYPE: nh)
(UNKNOWN ATOM TYPE: no)
(UNKNOWN ATOM TYPE: s2)
(UNKNOWN ATOM TYPE: s4)
(UNKNOWN ATOM TYPE: s6)
(UNKNOWN ATOM TYPE: sx)
(UNKNOWN ATOM TYPE: sy)
(UNKNOWN ATOM TYPE: ss)
(UNKNOWN ATOM TYPE: p2)
(UNKNOWN ATOM TYPE: p3)
(UNKNOWN ATOM TYPE: p4)
(UNKNOWN ATOM TYPE: p5)
(UNKNOWN ATOM TYPE: pb)
(UNKNOWN ATOM TYPE: px)
(UNKNOWN ATOM TYPE: py)
> heme = loadamberparams hemes3.frcmod
Loading parameters: ./hemes3.frcmod
Reading force field modification type file (frcmod)
Reading title:
  fe+3 heme: p450-o2 heme-no
Unknown keyword:            in parameter file.
 WARNING: expected Improper Torsion PK>0 (0.000000)
 Here is the Improper Torsion line in question:
X  hy c4 X    1       0.000     180.000       2.000
 WARNING: expected Improper Torsion PK>0 (0.000000)
 Here is the Improper Torsion line in question:
X  cf hz X    1       0.000     180.000       2.000
(UNKNOWN ATOM TYPE: lo)
(UNKNOWN ATOM TYPE: lw)
(UNKNOWN ATOM TYPE: o5)
(UNKNOWN ATOM TYPE: lc)
(UNKNOWN ATOM TYPE: ln)
(UNKNOWN ATOM TYPE: no)
(UNKNOWN ATOM TYPE: c5)
(UNKNOWN ATOM TYPE: c4)
(UNKNOWN ATOM TYPE: c1)
(UNKNOWN ATOM TYPE: he)
(UNKNOWN ATOM TYPE: hm)
(UNKNOWN ATOM TYPE: hk)
(UNKNOWN ATOM TYPE: hj)
(UNKNOWN ATOM TYPE: hy)
(UNKNOWN ATOM TYPE: hn)
(UNKNOWN ATOM TYPE: hz)
(UNKNOWN ATOM TYPE: lh)
> ions = loadamberparams frcmod_smith_dang
Loading parameters: ./frcmod_smith_dang
Reading force field modification type file (frcmod)
Reading title:
smith/dang ion parameters
(UNKNOWN ATOM TYPE: IM)
(UNKNOWN ATOM TYPE: IP)
> loadoff CYP.off
Loading library: ./CYP.off
Loading: CYP
> 
> gaffnew = loadamberparams Tmx_gaff.dat
Loading parameters: ./Tmx_gaff.dat
Reading title:
AMBER General Force Field for organic mol., add. info. at the end (June, 2003)
(UNKNOWN ATOM TYPE: hn)
(UNKNOWN ATOM TYPE: hx)
(UNKNOWN ATOM TYPE: c1)
(UNKNOWN ATOM TYPE: cu)
(UNKNOWN ATOM TYPE: cx)
(UNKNOWN ATOM TYPE: n1)
(UNKNOWN ATOM TYPE: n4)
(UNKNOWN ATOM TYPE: nd)
(UNKNOWN ATOM TYPE: ne)
(UNKNOWN ATOM TYPE: nf)
(UNKNOWN ATOM TYPE: nh)
(UNKNOWN ATOM TYPE: no)
(UNKNOWN ATOM TYPE: s2)
(UNKNOWN ATOM TYPE: s4)
(UNKNOWN ATOM TYPE: s6)
(UNKNOWN ATOM TYPE: sx)
(UNKNOWN ATOM TYPE: sy)
(UNKNOWN ATOM TYPE: ss)
(UNKNOWN ATOM TYPE: p2)
(UNKNOWN ATOM TYPE: p3)
(UNKNOWN ATOM TYPE: p4)
(UNKNOWN ATOM TYPE: p5)
(UNKNOWN ATOM TYPE: pb)
(UNKNOWN ATOM TYPE: px)
(UNKNOWN ATOM TYPE: py)
> frcmod = loadamberparams Tmx_f.frcmod
Loading parameters: ./Tmx_f.frcmod
Reading force field modification type file (frcmod)
Reading title:
REMARK 8/6 Modified Junmei frcmod 
Unknown keyword: REMARK ca- in parameter file.
> OHT = loadmol2 FOHT_1_RED_ac.mol2
Loading Mol2 file: ./FOHT_1_RED_ac.mol2
Reading MOLECULE named OHT
> 
> aa = loadpdb b12.pdb
Could not open file b12.pdb: not found
> 
> bond aa.415.SG aa.473.FE
bond: Argument #1 is type String must be of type: [atom]
usage:  bond <atom1> <atom2> [order]
> 
> saveamberparm aa b12_invacuo.topo b12_invacuo.coords
saveAmberParm: Argument #1 is type String must be of type: [unit]
usage:  saveAmberParm <unit> <topologyfile> <coordfile> 
> 
> solvateoct aa TIP3PBOX 12.0 iso
solvateOct: Argument #1 is type String must be of type: [unit]
usage:  solvateOct <solute> <solvent> <buffer> [aniso] [closeness]
> 
> addions aa Cl- 0
addIons: Argument #1 is type String must be of type: [unit]

    addIons unit ion1 #ion1 [ion2 #ion2]
 
	UNIT			_unit_
	UNIT			_ion1_
	NUMBER			_#ion1_
	UNIT			_ion2_
	NUMBER			_#ion2_
 
Adds counterions in a shell around _unit_ using a Coulombic potential
on a grid. If _#ion1_ is 0, the _unit_ is neutralized (_ion1_ must be
opposite in charge to _unit_, and _ion2_ cannot be specified). Otherwise,
the specified numbers of _ion1_ [_ion2_] are added [in alternating order].
If solvent is present, it is ignored in the charge and steric calculations,
and if an ion has a steric conflict with a solvent molecule, the ion is
moved to the center of said molecule, and the latter is deleted. (To
avoid this behavior, either solvate _after_ addions, or use addIons2.)
Ions must be monoatomic. Note that the one-at-a-time procedure is not
guaranteed to globally minimize the electrostatic energy. When neutralizing
regular-backbone nucleic acids, the first cations will generally be added 
between phosphates, leaving the final two ions to be placed somewhere around
the middle of the molecule.
The default grid resolution is 1 Angstrom, extending from an inner radius
of (max ion size + max solute atom size) to an outer radius 4 Angstroms
beyond. A distance-dependent dielectric is used for speed.


> 
> addions aa Na+ 10 Cl- 10
addIons: Argument #1 is type String must be of type: [unit]

    addIons unit ion1 #ion1 [ion2 #ion2]
 
	UNIT			_unit_
	UNIT			_ion1_
	NUMBER			_#ion1_
	UNIT			_ion2_
	NUMBER			_#ion2_
 
Adds counterions in a shell around _unit_ using a Coulombic potential
on a grid. If _#ion1_ is 0, the _unit_ is neutralized (_ion1_ must be
opposite in charge to _unit_, and _ion2_ cannot be specified). Otherwise,
the specified numbers of _ion1_ [_ion2_] are added [in alternating order].
If solvent is present, it is ignored in the charge and steric calculations,
and if an ion has a steric conflict with a solvent molecule, the ion is
moved to the center of said molecule, and the latter is deleted. (To
avoid this behavior, either solvate _after_ addions, or use addIons2.)
Ions must be monoatomic. Note that the one-at-a-time procedure is not
guaranteed to globally minimize the electrostatic energy. When neutralizing
regular-backbone nucleic acids, the first cations will generally be added 
between phosphates, leaving the final two ions to be placed somewhere around
the middle of the molecule.
The default grid resolution is 1 Angstrom, extending from an inner radius
of (max ion size + max solute atom size) to an outer radius 4 Angstroms
beyond. A distance-dependent dielectric is used for speed.


> addions aa Na+ 10 Cl- 10
addIons: Argument #1 is type String must be of type: [unit]

    addIons unit ion1 #ion1 [ion2 #ion2]
 
	UNIT			_unit_
	UNIT			_ion1_
	NUMBER			_#ion1_
	UNIT			_ion2_
	NUMBER			_#ion2_
 
Adds counterions in a shell around _unit_ using a Coulombic potential
on a grid. If _#ion1_ is 0, the _unit_ is neutralized (_ion1_ must be
opposite in charge to _unit_, and _ion2_ cannot be specified). Otherwise,
the specified numbers of _ion1_ [_ion2_] are added [in alternating order].
If solvent is present, it is ignored in the charge and steric calculations,
and if an ion has a steric conflict with a solvent molecule, the ion is
moved to the center of said molecule, and the latter is deleted. (To
avoid this behavior, either solvate _after_ addions, or use addIons2.)
Ions must be monoatomic. Note that the one-at-a-time procedure is not
guaranteed to globally minimize the electrostatic energy. When neutralizing
regular-backbone nucleic acids, the first cations will generally be added 
between phosphates, leaving the final two ions to be placed somewhere around
the middle of the molecule.
The default grid resolution is 1 Angstrom, extending from an inner radius
of (max ion size + max solute atom size) to an outer radius 4 Angstroms
beyond. A distance-dependent dielectric is used for speed.


> addions aa Na+ 10 Cl- 10
addIons: Argument #1 is type String must be of type: [unit]

    addIons unit ion1 #ion1 [ion2 #ion2]
 
	UNIT			_unit_
	UNIT			_ion1_
	NUMBER			_#ion1_
	UNIT			_ion2_
	NUMBER			_#ion2_
 
Adds counterions in a shell around _unit_ using a Coulombic potential
on a grid. If _#ion1_ is 0, the _unit_ is neutralized (_ion1_ must be
opposite in charge to _unit_, and _ion2_ cannot be specified). Otherwise,
the specified numbers of _ion1_ [_ion2_] are added [in alternating order].
If solvent is present, it is ignored in the charge and steric calculations,
and if an ion has a steric conflict with a solvent molecule, the ion is
moved to the center of said molecule, and the latter is deleted. (To
avoid this behavior, either solvate _after_ addions, or use addIons2.)
Ions must be monoatomic. Note that the one-at-a-time procedure is not
guaranteed to globally minimize the electrostatic energy. When neutralizing
regular-backbone nucleic acids, the first cations will generally be added 
between phosphates, leaving the final two ions to be placed somewhere around
the middle of the molecule.
The default grid resolution is 1 Angstrom, extending from an inner radius
of (max ion size + max solute atom size) to an outer radius 4 Angstroms
beyond. A distance-dependent dielectric is used for speed.


> addions aa Na+ 10 Cl- 10
addIons: Argument #1 is type String must be of type: [unit]

    addIons unit ion1 #ion1 [ion2 #ion2]
 
	UNIT			_unit_
	UNIT			_ion1_
	NUMBER			_#ion1_
	UNIT			_ion2_
	NUMBER			_#ion2_
 
Adds counterions in a shell around _unit_ using a Coulombic potential
on a grid. If _#ion1_ is 0, the _unit_ is neutralized (_ion1_ must be
opposite in charge to _unit_, and _ion2_ cannot be specified). Otherwise,
the specified numbers of _ion1_ [_ion2_] are added [in alternating order].
If solvent is present, it is ignored in the charge and steric calculations,
and if an ion has a steric conflict with a solvent molecule, the ion is
moved to the center of said molecule, and the latter is deleted. (To
avoid this behavior, either solvate _after_ addions, or use addIons2.)
Ions must be monoatomic. Note that the one-at-a-time procedure is not
guaranteed to globally minimize the electrostatic energy. When neutralizing
regular-backbone nucleic acids, the first cations will generally be added 
between phosphates, leaving the final two ions to be placed somewhere around
the middle of the molecule.
The default grid resolution is 1 Angstrom, extending from an inner radius
of (max ion size + max solute atom size) to an outer radius 4 Angstroms
beyond. A distance-dependent dielectric is used for speed.


> addions aa Na+ 10 Cl- 10
addIons: Argument #1 is type String must be of type: [unit]

    addIons unit ion1 #ion1 [ion2 #ion2]
 
	UNIT			_unit_
	UNIT			_ion1_
	NUMBER			_#ion1_
	UNIT			_ion2_
	NUMBER			_#ion2_
 
Adds counterions in a shell around _unit_ using a Coulombic potential
on a grid. If _#ion1_ is 0, the _unit_ is neutralized (_ion1_ must be
opposite in charge to _unit_, and _ion2_ cannot be specified). Otherwise,
the specified numbers of _ion1_ [_ion2_] are added [in alternating order].
If solvent is present, it is ignored in the charge and steric calculations,
and if an ion has a steric conflict with a solvent molecule, the ion is
moved to the center of said molecule, and the latter is deleted. (To
avoid this behavior, either solvate _after_ addions, or use addIons2.)
Ions must be monoatomic. Note that the one-at-a-time procedure is not
guaranteed to globally minimize the electrostatic energy. When neutralizing
regular-backbone nucleic acids, the first cations will generally be added 
between phosphates, leaving the final two ions to be placed somewhere around
the middle of the molecule.
The default grid resolution is 1 Angstrom, extending from an inner radius
of (max ion size + max solute atom size) to an outer radius 4 Angstroms
beyond. A distance-dependent dielectric is used for speed.


> addions aa Na+ 10 Cl- 10
addIons: Argument #1 is type String must be of type: [unit]

    addIons unit ion1 #ion1 [ion2 #ion2]
 
	UNIT			_unit_
	UNIT			_ion1_
	NUMBER			_#ion1_
	UNIT			_ion2_
	NUMBER			_#ion2_
 
Adds counterions in a shell around _unit_ using a Coulombic potential
on a grid. If _#ion1_ is 0, the _unit_ is neutralized (_ion1_ must be
opposite in charge to _unit_, and _ion2_ cannot be specified). Otherwise,
the specified numbers of _ion1_ [_ion2_] are added [in alternating order].
If solvent is present, it is ignored in the charge and steric calculations,
and if an ion has a steric conflict with a solvent molecule, the ion is
moved to the center of said molecule, and the latter is deleted. (To
avoid this behavior, either solvate _after_ addions, or use addIons2.)
Ions must be monoatomic. Note that the one-at-a-time procedure is not
guaranteed to globally minimize the electrostatic energy. When neutralizing
regular-backbone nucleic acids, the first cations will generally be added 
between phosphates, leaving the final two ions to be placed somewhere around
the middle of the molecule.
The default grid resolution is 1 Angstrom, extending from an inner radius
of (max ion size + max solute atom size) to an outer radius 4 Angstroms
beyond. A distance-dependent dielectric is used for speed.


> addions aa Na+ 10 Cl- 10
addIons: Argument #1 is type String must be of type: [unit]

    addIons unit ion1 #ion1 [ion2 #ion2]
 
	UNIT			_unit_
	UNIT			_ion1_
	NUMBER			_#ion1_
	UNIT			_ion2_
	NUMBER			_#ion2_
 
Adds counterions in a shell around _unit_ using a Coulombic potential
on a grid. If _#ion1_ is 0, the _unit_ is neutralized (_ion1_ must be
opposite in charge to _unit_, and _ion2_ cannot be specified). Otherwise,
the specified numbers of _ion1_ [_ion2_] are added [in alternating order].
If solvent is present, it is ignored in the charge and steric calculations,
and if an ion has a steric conflict with a solvent molecule, the ion is
moved to the center of said molecule, and the latter is deleted. (To
avoid this behavior, either solvate _after_ addions, or use addIons2.)
Ions must be monoatomic. Note that the one-at-a-time procedure is not
guaranteed to globally minimize the electrostatic energy. When neutralizing
regular-backbone nucleic acids, the first cations will generally be added 
between phosphates, leaving the final two ions to be placed somewhere around
the middle of the molecule.
The default grid resolution is 1 Angstrom, extending from an inner radius
of (max ion size + max solute atom size) to an outer radius 4 Angstroms
beyond. A distance-dependent dielectric is used for speed.


> 
> saveamberparm aa b12.topo b12.coords
saveAmberParm: Argument #1 is type String must be of type: [unit]
usage:  saveAmberParm <unit> <topologyfile> <coordfile> 
> 
 
> quit
	Quit
log started: Fri Aug 15 12:56:31 2008

Log file: ./leap.log
> #
> # ----- leaprc for loading the ff99SB (Hornak & Simmerling) force field
> #
> #	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" }
> 	{ "OH"  "O" "sp3" }
> 	{ "OS"  "O" "sp3" }
> 	{ "O"   "O" "sp2" }
> 	{ "O2"  "O" "sp2" }
> 	{ "OW"  "O" "sp3" }
> 	{ "CT"  "C" "sp3" }
> 	{ "CH"  "C" "sp3" }
> 	{ "C2"  "C" "sp3" }
> 	{ "C3"  "C" "sp3" }
> 	{ "C"   "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" }
> 	{ "CE"  "C" "sp2" }
> 	{ "CF"  "C" "sp2" }
> 	{ "CG"  "C" "sp2" }
> 	{ "CP"  "C" "sp2" }
> 	{ "CI"  "C" "sp2" }
> 	{ "CJ"  "C" "sp2" }
> 	{ "CW"  "C" "sp2" }
> 	{ "CV"  "C" "sp2" }
> 	{ "CR"  "C" "sp2" }
> 	{ "CA"  "C" "sp2" }
> 	{ "CY"  "C" "sp2" }
> 	{ "C0"  "C" "sp2" }
> 	{ "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" }
> 	{ "N3"  "N" "sp3" }
> 	{ "S"   "S" "sp3" }
> 	{ "SH"  "S" "sp3" }
> 	{ "P"   "P" "sp3" }
> 	{ "LP"  ""  "sp3" }
> 	{ "F"   "F" "sp3" }
> 	{ "CL"  "Cl" "sp3" }
> 	{ "BR"  "Br" "sp3" }
> 	{ "I"   "I"  "sp3" }
> 	{ "FE"  "Fe" "sp3" }
> 	{ "EP"  ""  "sp3" }
> # glycam
> 	{ "OG"  "O" "sp3" }
> 	{ "OL"  "O" "sp3" }
> 	{ "AC"  "C" "sp3" }
> 	{ "EC"  "C" "sp3" }
> }
> #
> #	Load the main parameter set.
> #
> parm99 = loadamberparams parm99.dat
Loading parameters: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/parm/parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99
(UNKNOWN ATOM TYPE: HZ)
(UNKNOWN ATOM TYPE: NY)
(UNKNOWN ATOM TYPE: IM)
(UNKNOWN ATOM TYPE: Li)
(UNKNOWN ATOM TYPE: IP)
(UNKNOWN ATOM TYPE: K)
(UNKNOWN ATOM TYPE: Rb)
(UNKNOWN ATOM TYPE: Cs)
(UNKNOWN ATOM TYPE: Zn)
(UNKNOWN ATOM TYPE: IB)
(UNKNOWN ATOM TYPE: LP)
> frcmod99SB = loadamberparams frcmod.ff99SB
Loading parameters: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/parm/frcmod.ff99SB
Reading force field modification type file (frcmod)
Reading title:
Modification/update of parm99.dat (Hornak & Simmerling)
> #
> #	Load DNA/RNA libraries
> #
> loadOff all_nucleic94.lib
Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/all_nucleic94.lib
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: RA
Loading: RA3
Loading: RA5
Loading: RAN
Loading: RC
Loading: RC3
Loading: RC5
Loading: RCN
Loading: RG
Loading: RG3
Loading: RG5
Loading: RGN
Loading: RU
Loading: RU3
Loading: RU5
Loading: RUN
> #
> #	Load main chain and terminating 
> #	amino acid libraries (i.e. ff94 libs)
> #
> loadOff all_amino94.lib
Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/all_amino94.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: ILE
Loading: LEU
Loading: LYN
Loading: LYS
Loading: MET
Loading: PHE
Loading: PRO
Loading: SER
Loading: THR
Loading: TRP
Loading: TYR
Loading: VAL
> loadOff all_aminoct94.lib
Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/all_aminoct94.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: 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 all_aminont94.lib
Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/all_aminont94.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
> #
> #       Load water and ions
> # 
> loadOff ions94.lib
Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/ions94.lib
Loading: CIO
Loading: Cl-
Loading: Cs+
Loading: IB
Loading: K+
Loading: Li+
Loading: MG2
Loading: Na+
Loading: Rb+
> loadOff solvents.lib
Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: MEOHBOX
Loading: NMABOX
Loading: PL3
Loading: POL3BOX
Loading: SPC
Loading: SPCBOX
Loading: SPCFWBOX
Loading: SPF
Loading: T4E
Loading: TIP3PBOX
Loading: TIP4PBOX
Loading: TIP4PEWBOX
Loading: TP3
Loading: TP4
Loading: TP5
> HOH = TP3
> WAT = TP3
> 
> #
> #	Define the PDB name map for the amino acids and DNA.
> #
> addPdbResMap {
>   { 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 "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" }
>   { 0 "G" "DG5"  } { 1 "G" "DG3"  } { "G" "DG" } { "GN" "DGN" }
>   { 0 "A" "DA5"  } { 1 "A" "DA3"  } { "A" "DA" } { "AN" "DAN" }
>   { 0 "C" "DC5"  } { 1 "C" "DC3"  } { "C" "DC" } { "CN" "DCN" }
>   { 0 "T" "DT5"  } { 1 "T" "DT3"  } { "T" "DT" } { "TN" "DTN" }
>   { 0 "C5" "DC5" }
>   { 0 "G5" "DG5" }
>   { 0 "A5" "DA5" }
>   { 0 "T5" "DT5" }
>   { 1 "C3" "DC3" }
>   { 1 "G3" "DG3" }
>   { 1 "A3" "DA3" }
>   { 1 "T3" "DT3" }
> 
> }
> 
> addPdbAtomMap {
>   { "O5*" "O5'" }
>   { "C5*" "C5'" }
>   { "C4*" "C4'" }
>   { "O4*" "O4'" }
>   { "C3*" "C3'" }
>   { "O3*" "O3'" }
>   { "C2*" "C2'" }
>   { "C1*" "C1'" }
>   { "C5M" "C7"  }
>   { "H1*" "H1'" }
>   { "H2*1" "H2'1" }
>   { "H2*2" "H2'2" }
>   { "H3*" "H3'" }
>   { "H4*" "H4'" }
>   { "H5*1" "H5'1" }
>   { "H5*2" "H5'2" }
> # old ff atom names -> new
>   { "O1'" "O4'" }
>   { "OA"  "O1P" }
>   { "OB"  "O2P" }
> }
> 
> 
> #
> # assumed that most often proteins use HIE
> #
> NHIS = NHIE
> HIS = HIE
> CHIS = CHIE
 
Sourcing: ./buildit
> 
> #CM5 = loadmol2 cm5.mol2
> #TMI = loadmol2 tmi.mol2
> loadoff heme.off
Loading library: ./heme.off
Loading: HEM
> gaff = loadamberparams gaff.dat
Loading parameters: ./gaff.dat
Reading title:
AMBER General Force Field for organic mol., add. info. at the end (June, 2003)
(UNKNOWN ATOM TYPE: hn)
(UNKNOWN ATOM TYPE: hx)
(UNKNOWN ATOM TYPE: c1)
(UNKNOWN ATOM TYPE: cu)
(UNKNOWN ATOM TYPE: cx)
(UNKNOWN ATOM TYPE: n1)
(UNKNOWN ATOM TYPE: n4)
(UNKNOWN ATOM TYPE: nd)
(UNKNOWN ATOM TYPE: ne)
(UNKNOWN ATOM TYPE: nf)
(UNKNOWN ATOM TYPE: nh)
(UNKNOWN ATOM TYPE: no)
(UNKNOWN ATOM TYPE: s2)
(UNKNOWN ATOM TYPE: s4)
(UNKNOWN ATOM TYPE: s6)
(UNKNOWN ATOM TYPE: sx)
(UNKNOWN ATOM TYPE: sy)
(UNKNOWN ATOM TYPE: ss)
(UNKNOWN ATOM TYPE: p2)
(UNKNOWN ATOM TYPE: p3)
(UNKNOWN ATOM TYPE: p4)
(UNKNOWN ATOM TYPE: p5)
(UNKNOWN ATOM TYPE: pb)
(UNKNOWN ATOM TYPE: px)
(UNKNOWN ATOM TYPE: py)
> heme = loadamberparams hemes3.frcmod
Loading parameters: ./hemes3.frcmod
Reading force field modification type file (frcmod)
Reading title:
  fe+3 heme: p450-o2 heme-no
Unknown keyword:            in parameter file.
 WARNING: expected Improper Torsion PK>0 (0.000000)
 Here is the Improper Torsion line in question:
X  hy c4 X    1       0.000     180.000       2.000
 WARNING: expected Improper Torsion PK>0 (0.000000)
 Here is the Improper Torsion line in question:
X  cf hz X    1       0.000     180.000       2.000
(UNKNOWN ATOM TYPE: lo)
(UNKNOWN ATOM TYPE: lw)
(UNKNOWN ATOM TYPE: o5)
(UNKNOWN ATOM TYPE: lc)
(UNKNOWN ATOM TYPE: ln)
(UNKNOWN ATOM TYPE: no)
(UNKNOWN ATOM TYPE: c5)
(UNKNOWN ATOM TYPE: c4)
(UNKNOWN ATOM TYPE: c1)
(UNKNOWN ATOM TYPE: he)
(UNKNOWN ATOM TYPE: hm)
(UNKNOWN ATOM TYPE: hk)
(UNKNOWN ATOM TYPE: hj)
(UNKNOWN ATOM TYPE: hy)
(UNKNOWN ATOM TYPE: hn)
(UNKNOWN ATOM TYPE: hz)
(UNKNOWN ATOM TYPE: lh)
> ions = loadamberparams frcmod_smith_dang
Loading parameters: ./frcmod_smith_dang
Reading force field modification type file (frcmod)
Reading title:
smith/dang ion parameters
(UNKNOWN ATOM TYPE: IM)
(UNKNOWN ATOM TYPE: IP)
> loadoff CYP.off
Loading library: ./CYP.off
Loading: CYP
> 
> gaffnew = loadamberparams Tmx_gaff.dat
Loading parameters: ./Tmx_gaff.dat
Reading title:
AMBER General Force Field for organic mol., add. info. at the end (June, 2003)
(UNKNOWN ATOM TYPE: hn)
(UNKNOWN ATOM TYPE: hx)
(UNKNOWN ATOM TYPE: c1)
(UNKNOWN ATOM TYPE: cu)
(UNKNOWN ATOM TYPE: cx)
(UNKNOWN ATOM TYPE: n1)
(UNKNOWN ATOM TYPE: n4)
(UNKNOWN ATOM TYPE: nd)
(UNKNOWN ATOM TYPE: ne)
(UNKNOWN ATOM TYPE: nf)
(UNKNOWN ATOM TYPE: nh)
(UNKNOWN ATOM TYPE: no)
(UNKNOWN ATOM TYPE: s2)
(UNKNOWN ATOM TYPE: s4)
(UNKNOWN ATOM TYPE: s6)
(UNKNOWN ATOM TYPE: sx)
(UNKNOWN ATOM TYPE: sy)
(UNKNOWN ATOM TYPE: ss)
(UNKNOWN ATOM TYPE: p2)
(UNKNOWN ATOM TYPE: p3)
(UNKNOWN ATOM TYPE: p4)
(UNKNOWN ATOM TYPE: p5)
(UNKNOWN ATOM TYPE: pb)
(UNKNOWN ATOM TYPE: px)
(UNKNOWN ATOM TYPE: py)
> frcmod = loadamberparams Tmx_f.frcmod
Loading parameters: ./Tmx_f.frcmod
Reading force field modification type file (frcmod)
Reading title:
REMARK 8/6 Modified Junmei frcmod 
Unknown keyword: REMARK ca- in parameter file.
> OHT = loadmol2 FOHT_1_RED_ac.mol2
Loading Mol2 file: ./FOHT_1_RED_ac.mol2
Reading MOLECULE named OHT
> 
> aa = loadpdb b13.pdb
Loading PDB file: ./b13.pdb
Enter zPdbReadScan from call depth  0.
Exit  zPdbReadScan from call depth  0.
Matching PDB residue names to LEaP variables.
Mapped residue HIE, term: Terminal/beginning, seq. number: 0 to: NHIE.
(Residue 1: SER, Nonterminal, was not found in name map.)
(Residue 2: HIE, Nonterminal, was not found in name map.)
(Residue 3: GLY, Nonterminal, was not found in name map.)
(Residue 4: LEU, Nonterminal, was not found in name map.)
(Residue 5: PHE, Nonterminal, was not found in name map.)
(Residue 6: LYS, Nonterminal, was not found in name map.)
(Residue 7: LYS, Nonterminal, was not found in name map.)
(Residue 8: LEU, Nonterminal, was not found in name map.)
(Residue 9: GLY, Nonterminal, was not found in name map.)
(Residue 10: ILE, Nonterminal, was not found in name map.)
(Residue 11: PRO, Nonterminal, was not found in name map.)
(Residue 12: GLY, Nonterminal, was not found in name map.)
(Residue 13: PRO, Nonterminal, was not found in name map.)
(Residue 14: THR, Nonterminal, was not found in name map.)
(Residue 15: PRO, Nonterminal, was not found in name map.)
(Residue 16: LEU, Nonterminal, was not found in name map.)
(Residue 17: PRO, Nonterminal, was not found in name map.)
(Residue 18: PHE, Nonterminal, was not found in name map.)
(Residue 19: LEU, Nonterminal, was not found in name map.)
(Residue 20: GLY, Nonterminal, was not found in name map.)
(Residue 21: ASN, Nonterminal, was not found in name map.)
(Residue 22: ILE, Nonterminal, was not found in name map.)
(Residue 23: LEU, Nonterminal, was not found in name map.)
(Residue 24: SER, Nonterminal, was not found in name map.)
(Residue 25: TYR, Nonterminal, was not found in name map.)
(Residue 26: HID, Nonterminal, was not found in name map.)
(Residue 27: LYS, Nonterminal, was not found in name map.)
(Residue 28: GLY, Nonterminal, was not found in name map.)
(Residue 29: PHE, Nonterminal, was not found in name map.)
(Residue 30: CYS, Nonterminal, was not found in name map.)
(Residue 31: MET, Nonterminal, was not found in name map.)
(Residue 32: PHE, Nonterminal, was not found in name map.)
(Residue 33: ASP, Nonterminal, was not found in name map.)
(Residue 34: MET, Nonterminal, was not found in name map.)
(Residue 35: GLU, Nonterminal, was not found in name map.)
(Residue 36: CYS, Nonterminal, was not found in name map.)
(Residue 37: HIE, Nonterminal, was not found in name map.)
(Residue 38: LYS, Nonterminal, was not found in name map.)
(Residue 39: LYS, Nonterminal, was not found in name map.)
(Residue 40: TYR, Nonterminal, was not found in name map.)
(Residue 41: GLY, Nonterminal, was not found in name map.)
(Residue 42: LYS, Nonterminal, was not found in name map.)
(Residue 43: VAL, Nonterminal, was not found in name map.)
(Residue 44: TRP, Nonterminal, was not found in name map.)
(Residue 45: GLY, Nonterminal, was not found in name map.)
(Residue 46: PHE, Nonterminal, was not found in name map.)
(Residue 47: TYR, Nonterminal, was not found in name map.)
(Residue 48: ASP, Nonterminal, was not found in name map.)
(Residue 49: GLY, Nonterminal, was not found in name map.)
(Residue 50: GLN, Nonterminal, was not found in name map.)
(Residue 51: GLN, Nonterminal, was not found in name map.)
(Residue 52: PRO, Nonterminal, was not found in name map.)
(Residue 53: VAL, Nonterminal, was not found in name map.)
(Residue 54: LEU, Nonterminal, was not found in name map.)
(Residue 55: ALA, Nonterminal, was not found in name map.)
(Residue 56: ILE, Nonterminal, was not found in name map.)
(Residue 57: THR, Nonterminal, was not found in name map.)
(Residue 58: ASP, Nonterminal, was not found in name map.)
(Residue 59: PRO, Nonterminal, was not found in name map.)
(Residue 60: ASP, Nonterminal, was not found in name map.)
(Residue 61: MET, Nonterminal, was not found in name map.)
(Residue 62: ILE, Nonterminal, was not found in name map.)
(Residue 63: LYS, Nonterminal, was not found in name map.)
(Residue 64: THR, Nonterminal, was not found in name map.)
(Residue 65: VAL, Nonterminal, was not found in name map.)
(Residue 66: LEU, Nonterminal, was not found in name map.)
(Residue 67: VAL, Nonterminal, was not found in name map.)
(Residue 68: LYS, Nonterminal, was not found in name map.)
(Residue 69: GLU, Nonterminal, was not found in name map.)
(Residue 70: CYS, Nonterminal, was not found in name map.)
(Residue 71: TYR, Nonterminal, was not found in name map.)
(Residue 72: SER, Nonterminal, was not found in name map.)
(Residue 73: VAL, Nonterminal, was not found in name map.)
(Residue 74: PHE, Nonterminal, was not found in name map.)
(Residue 75: THR, Nonterminal, was not found in name map.)
(Residue 76: ASN, Nonterminal, was not found in name map.)
(Residue 77: ARG, Nonterminal, was not found in name map.)
(Residue 78: ARG, Nonterminal, was not found in name map.)
(Residue 79: PRO, Nonterminal, was not found in name map.)
(Residue 80: PHE, Nonterminal, was not found in name map.)
(Residue 81: GLY, Nonterminal, was not found in name map.)
(Residue 82: PRO, Nonterminal, was not found in name map.)
(Residue 83: VAL, Nonterminal, was not found in name map.)
(Residue 84: GLY, Nonterminal, was not found in name map.)
(Residue 85: PHE, Nonterminal, was not found in name map.)
(Residue 86: MET, Nonterminal, was not found in name map.)
(Residue 87: LYS, Nonterminal, was not found in name map.)
(Residue 88: SER, Nonterminal, was not found in name map.)
(Residue 89: ALA, Nonterminal, was not found in name map.)
(Residue 90: ILE, Nonterminal, was not found in name map.)
(Residue 91: SER, Nonterminal, was not found in name map.)
(Residue 92: ILE, Nonterminal, was not found in name map.)
(Residue 93: ALA, Nonterminal, was not found in name map.)
(Residue 94: GLU, Nonterminal, was not found in name map.)
(Residue 95: ASP, Nonterminal, was not found in name map.)
(Residue 96: GLU, Nonterminal, was not found in name map.)
(Residue 97: GLU, Nonterminal, was not found in name map.)
(Residue 98: TRP, Nonterminal, was not found in name map.)
(Residue 99: LYS, Nonterminal, was not found in name map.)
(Residue 100: ARG, Nonterminal, was not found in name map.)
(Residue 101: LEU, Nonterminal, was not found in name map.)
(Residue 102: ARG, Nonterminal, was not found in name map.)
(Residue 103: SER, Nonterminal, was not found in name map.)
(Residue 104: LEU, Nonterminal, was not found in name map.)
(Residue 105: LEU, Nonterminal, was not found in name map.)
(Residue 106: SER, Nonterminal, was not found in name map.)
(Residue 107: PRO, Nonterminal, was not found in name map.)
(Residue 108: THR, Nonterminal, was not found in name map.)
(Residue 109: PHE, Nonterminal, was not found in name map.)
(Residue 110: THR, Nonterminal, was not found in name map.)
(Residue 111: SER, Nonterminal, was not found in name map.)
(Residue 112: GLY, Nonterminal, was not found in name map.)
(Residue 113: LYS, Nonterminal, was not found in name map.)
(Residue 114: LEU, Nonterminal, was not found in name map.)
(Residue 115: LYS, Nonterminal, was not found in name map.)
(Residue 116: GLU, Nonterminal, was not found in name map.)
(Residue 117: MET, Nonterminal, was not found in name map.)
(Residue 118: VAL, Nonterminal, was not found in name map.)
(Residue 119: PRO, Nonterminal, was not found in name map.)
(Residue 120: ILE, Nonterminal, was not found in name map.)
(Residue 121: ILE, Nonterminal, was not found in name map.)
(Residue 122: ALA, Nonterminal, was not found in name map.)
(Residue 123: GLN, Nonterminal, was not found in name map.)
(Residue 124: TYR, Nonterminal, was not found in name map.)
(Residue 125: GLY, Nonterminal, was not found in name map.)
(Residue 126: ASP, Nonterminal, was not found in name map.)
(Residue 127: VAL, Nonterminal, was not found in name map.)
(Residue 128: LEU, Nonterminal, was not found in name map.)
(Residue 129: VAL, Nonterminal, was not found in name map.)
(Residue 130: ARG, Nonterminal, was not found in name map.)
(Residue 131: ASN, Nonterminal, was not found in name map.)
(Residue 132: LEU, Nonterminal, was not found in name map.)
(Residue 133: ARG, Nonterminal, was not found in name map.)
(Residue 134: ARG, Nonterminal, was not found in name map.)
(Residue 135: GLU, Nonterminal, was not found in name map.)
(Residue 136: ALA, Nonterminal, was not found in name map.)
(Residue 137: GLU, Nonterminal, was not found in name map.)
(Residue 138: THR, Nonterminal, was not found in name map.)
(Residue 139: GLY, Nonterminal, was not found in name map.)
(Residue 140: LYS, Nonterminal, was not found in name map.)
(Residue 141: PRO, Nonterminal, was not found in name map.)
(Residue 142: VAL, Nonterminal, was not found in name map.)
(Residue 143: THR, Nonterminal, was not found in name map.)
(Residue 144: LEU, Nonterminal, was not found in name map.)
(Residue 145: LYS, Nonterminal, was not found in name map.)
(Residue 146: ASP, Nonterminal, was not found in name map.)
(Residue 147: VAL, Nonterminal, was not found in name map.)
(Residue 148: PHE, Nonterminal, was not found in name map.)
(Residue 149: GLY, Nonterminal, was not found in name map.)
(Residue 150: ALA, Nonterminal, was not found in name map.)
(Residue 151: TYR, Nonterminal, was not found in name map.)
(Residue 152: SER, Nonterminal, was not found in name map.)
(Residue 153: MET, Nonterminal, was not found in name map.)
(Residue 154: ASP, Nonterminal, was not found in name map.)
(Residue 155: VAL, Nonterminal, was not found in name map.)
(Residue 156: ILE, Nonterminal, was not found in name map.)
(Residue 157: THR, Nonterminal, was not found in name map.)
(Residue 158: SER, Nonterminal, was not found in name map.)
(Residue 159: THR, Nonterminal, was not found in name map.)
(Residue 160: SER, Nonterminal, was not found in name map.)
(Residue 161: PHE, Nonterminal, was not found in name map.)
(Residue 162: GLY, Nonterminal, was not found in name map.)
(Residue 163: VAL, Nonterminal, was not found in name map.)
(Residue 164: ASN, Nonterminal, was not found in name map.)
(Residue 165: ILE, Nonterminal, was not found in name map.)
(Residue 166: ASP, Nonterminal, was not found in name map.)
(Residue 167: SER, Nonterminal, was not found in name map.)
(Residue 168: LEU, Nonterminal, was not found in name map.)
(Residue 169: ASN, Nonterminal, was not found in name map.)
(Residue 170: ASN, Nonterminal, was not found in name map.)
(Residue 171: PRO, Nonterminal, was not found in name map.)
(Residue 172: GLN, Nonterminal, was not found in name map.)
(Residue 173: ASP, Nonterminal, was not found in name map.)
(Residue 174: PRO, Nonterminal, was not found in name map.)
(Residue 175: PHE, Nonterminal, was not found in name map.)
(Residue 176: VAL, Nonterminal, was not found in name map.)
(Residue 177: GLU, Nonterminal, was not found in name map.)
(Residue 178: ASN, Nonterminal, was not found in name map.)
(Residue 179: THR, Nonterminal, was not found in name map.)
(Residue 180: LYS, Nonterminal, was not found in name map.)
(Residue 181: LYS, Nonterminal, was not found in name map.)
(Residue 182: LEU, Nonterminal, was not found in name map.)
(Residue 183: LEU, Nonterminal, was not found in name map.)
(Residue 184: ARG, Nonterminal, was not found in name map.)
(Residue 185: PHE, Nonterminal, was not found in name map.)
(Residue 186: ASP, Nonterminal, was not found in name map.)
(Residue 187: PHE, Nonterminal, was not found in name map.)
(Residue 188: LEU, Nonterminal, was not found in name map.)
(Residue 189: ASP, Nonterminal, was not found in name map.)
(Residue 190: PRO, Nonterminal, was not found in name map.)
(Residue 191: PHE, Nonterminal, was not found in name map.)
(Residue 192: PHE, Nonterminal, was not found in name map.)
(Residue 193: LEU, Nonterminal, was not found in name map.)
(Residue 194: SER, Nonterminal, was not found in name map.)
(Residue 195: ILE, Nonterminal, was not found in name map.)
(Residue 196: THR, Nonterminal, was not found in name map.)
(Residue 197: VAL, Nonterminal, was not found in name map.)
(Residue 198: PHE, Nonterminal, was not found in name map.)
(Residue 199: PRO, Nonterminal, was not found in name map.)
(Residue 200: PHE, Nonterminal, was not found in name map.)
(Residue 201: LEU, Nonterminal, was not found in name map.)
(Residue 202: ILE, Nonterminal, was not found in name map.)
(Residue 203: PRO, Nonterminal, was not found in name map.)
(Residue 204: ILE, Nonterminal, was not found in name map.)
(Residue 205: LEU, Nonterminal, was not found in name map.)
(Residue 206: GLU, Nonterminal, was not found in name map.)
(Residue 207: VAL, Nonterminal, was not found in name map.)
(Residue 208: LEU, Nonterminal, was not found in name map.)
(Residue 209: ASN, Nonterminal, was not found in name map.)
(Residue 210: ILE, Nonterminal, was not found in name map.)
(Residue 211: CYS, Nonterminal, was not found in name map.)
(Residue 212: VAL, Nonterminal, was not found in name map.)
(Residue 213: PHE, Nonterminal, was not found in name map.)
(Residue 214: PRO, Nonterminal, was not found in name map.)
(Residue 215: ARG, Nonterminal, was not found in name map.)
(Residue 216: GLU, Nonterminal, was not found in name map.)
(Residue 217: VAL, Nonterminal, was not found in name map.)
(Residue 218: THR, Nonterminal, was not found in name map.)
(Residue 219: ASN, Nonterminal, was not found in name map.)
(Residue 220: PHE, Nonterminal, was not found in name map.)
(Residue 221: LEU, Nonterminal, was not found in name map.)
(Residue 222: ARG, Nonterminal, was not found in name map.)
(Residue 223: LYS, Nonterminal, was not found in name map.)
(Residue 224: SER, Nonterminal, was not found in name map.)
(Residue 225: VAL, Nonterminal, was not found in name map.)
(Residue 226: LYS, Nonterminal, was not found in name map.)
(Residue 227: ARG, Nonterminal, was not found in name map.)
(Residue 228: MET, Nonterminal, was not found in name map.)
(Residue 229: LYS, Nonterminal, was not found in name map.)
(Residue 230: GLU, Nonterminal, was not found in name map.)
(Residue 231: SER, Nonterminal, was not found in name map.)
(Residue 232: ARG, Nonterminal, was not found in name map.)
(Residue 233: LEU, Nonterminal, was not found in name map.)
(Residue 234: GLU, Nonterminal, was not found in name map.)
(Residue 235: ASP, Nonterminal, was not found in name map.)
(Residue 236: THR, Nonterminal, was not found in name map.)
(Residue 237: GLN, Nonterminal, was not found in name map.)
(Residue 238: LYS, Nonterminal, was not found in name map.)
(Residue 239: HIE, Nonterminal, was not found in name map.)
(Residue 240: ARG, Nonterminal, was not found in name map.)
(Residue 241: VAL, Nonterminal, was not found in name map.)
(Residue 242: ASP, Nonterminal, was not found in name map.)
(Residue 243: PHE, Nonterminal, was not found in name map.)
(Residue 244: LEU, Nonterminal, was not found in name map.)
(Residue 245: GLN, Nonterminal, was not found in name map.)
(Residue 246: LEU, Nonterminal, was not found in name map.)
(Residue 247: MET, Nonterminal, was not found in name map.)
(Residue 248: ILE, Nonterminal, was not found in name map.)
(Residue 249: ASP, Nonterminal, was not found in name map.)
(Residue 250: SER, Nonterminal, was not found in name map.)
(Residue 251: GLN, Nonterminal, was not found in name map.)
(Residue 252: ASN, Nonterminal, was not found in name map.)
(Residue 253: SER, Nonterminal, was not found in name map.)
(Residue 254: LYS, Nonterminal, was not found in name map.)
(Residue 255: GLU, Nonterminal, was not found in name map.)
(Residue 256: THR, Nonterminal, was not found in name map.)
(Residue 257: GLU, Nonterminal, was not found in name map.)
(Residue 258: SER, Nonterminal, was not found in name map.)
(Residue 259: HIE, Nonterminal, was not found in name map.)
(Residue 260: LYS, Nonterminal, was not found in name map.)
(Residue 261: ALA, Nonterminal, was not found in name map.)
(Residue 262: LEU, Nonterminal, was not found in name map.)
(Residue 263: SER, Nonterminal, was not found in name map.)
(Residue 264: ASP, Nonterminal, was not found in name map.)
(Residue 265: LEU, Nonterminal, was not found in name map.)
(Residue 266: GLU, Nonterminal, was not found in name map.)
(Residue 267: LEU, Nonterminal, was not found in name map.)
(Residue 268: VAL, Nonterminal, was not found in name map.)
(Residue 269: ALA, Nonterminal, was not found in name map.)
(Residue 270: GLN, Nonterminal, was not found in name map.)
(Residue 271: SER, Nonterminal, was not found in name map.)
(Residue 272: ILE, Nonterminal, was not found in name map.)
(Residue 273: ILE, Nonterminal, was not found in name map.)
(Residue 274: PHE, Nonterminal, was not found in name map.)
(Residue 275: ILE, Nonterminal, was not found in name map.)
(Residue 276: PHE, Nonterminal, was not found in name map.)
(Residue 277: ALA, Nonterminal, was not found in name map.)
(Residue 278: GLY, Nonterminal, was not found in name map.)
(Residue 279: TYR, Nonterminal, was not found in name map.)
(Residue 280: GLU, Nonterminal, was not found in name map.)
(Residue 281: THR, Nonterminal, was not found in name map.)
(Residue 282: THR, Nonterminal, was not found in name map.)
(Residue 283: SER, Nonterminal, was not found in name map.)
(Residue 284: SER, Nonterminal, was not found in name map.)
(Residue 285: VAL, Nonterminal, was not found in name map.)
(Residue 286: LEU, Nonterminal, was not found in name map.)
(Residue 287: SER, Nonterminal, was not found in name map.)
(Residue 288: PHE, Nonterminal, was not found in name map.)
(Residue 289: ILE, Nonterminal, was not found in name map.)
(Residue 290: MET, Nonterminal, was not found in name map.)
(Residue 291: TYR, Nonterminal, was not found in name map.)
(Residue 292: GLU, Nonterminal, was not found in name map.)
(Residue 293: LEU, Nonterminal, was not found in name map.)
(Residue 294: ALA, Nonterminal, was not found in name map.)
(Residue 295: THR, Nonterminal, was not found in name map.)
(Residue 296: HIE, Nonterminal, was not found in name map.)
(Residue 297: PRO, Nonterminal, was not found in name map.)
(Residue 298: ASP, Nonterminal, was not found in name map.)
(Residue 299: VAL, Nonterminal, was not found in name map.)
(Residue 300: GLN, Nonterminal, was not found in name map.)
(Residue 301: GLN, Nonterminal, was not found in name map.)
(Residue 302: LYS, Nonterminal, was not found in name map.)
(Residue 303: LEU, Nonterminal, was not found in name map.)
(Residue 304: GLN, Nonterminal, was not found in name map.)
(Residue 305: GLU, Nonterminal, was not found in name map.)
(Residue 306: GLU, Nonterminal, was not found in name map.)
(Residue 307: ILE, Nonterminal, was not found in name map.)
(Residue 308: ASP, Nonterminal, was not found in name map.)
(Residue 309: ALA, Nonterminal, was not found in name map.)
(Residue 310: VAL, Nonterminal, was not found in name map.)
(Residue 311: LEU, Nonterminal, was not found in name map.)
(Residue 312: PRO, Nonterminal, was not found in name map.)
(Residue 313: ASN, Nonterminal, was not found in name map.)
(Residue 314: LYS, Nonterminal, was not found in name map.)
(Residue 315: ALA, Nonterminal, was not found in name map.)
(Residue 316: PRO, Nonterminal, was not found in name map.)
(Residue 317: PRO, Nonterminal, was not found in name map.)
(Residue 318: THR, Nonterminal, was not found in name map.)
(Residue 319: TYR, Nonterminal, was not found in name map.)
(Residue 320: ASP, Nonterminal, was not found in name map.)
(Residue 321: THR, Nonterminal, was not found in name map.)
(Residue 322: VAL, Nonterminal, was not found in name map.)
(Residue 323: LEU, Nonterminal, was not found in name map.)
(Residue 324: GLN, Nonterminal, was not found in name map.)
(Residue 325: MET, Nonterminal, was not found in name map.)
(Residue 326: GLU, Nonterminal, was not found in name map.)
(Residue 327: TYR, Nonterminal, was not found in name map.)
(Residue 328: LEU, Nonterminal, was not found in name map.)
(Residue 329: ASP, Nonterminal, was not found in name map.)
(Residue 330: MET, Nonterminal, was not found in name map.)
(Residue 331: VAL, Nonterminal, was not found in name map.)
(Residue 332: VAL, Nonterminal, was not found in name map.)
(Residue 333: ASN, Nonterminal, was not found in name map.)
(Residue 334: GLU, Nonterminal, was not found in name map.)
(Residue 335: THR, Nonterminal, was not found in name map.)
(Residue 336: LEU, Nonterminal, was not found in name map.)
(Residue 337: ARG, Nonterminal, was not found in name map.)
(Residue 338: LEU, Nonterminal, was not found in name map.)
(Residue 339: PHE, Nonterminal, was not found in name map.)
(Residue 340: PRO, Nonterminal, was not found in name map.)
(Residue 341: ILE, Nonterminal, was not found in name map.)
(Residue 342: ALA, Nonterminal, was not found in name map.)
(Residue 343: MET, Nonterminal, was not found in name map.)
(Residue 344: ARG, Nonterminal, was not found in name map.)
(Residue 345: LEU, Nonterminal, was not found in name map.)
(Residue 346: GLU, Nonterminal, was not found in name map.)
(Residue 347: ARG, Nonterminal, was not found in name map.)
(Residue 348: VAL, Nonterminal, was not found in name map.)
(Residue 349: CYS, Nonterminal, was not found in name map.)
(Residue 350: LYS, Nonterminal, was not found in name map.)
(Residue 351: LYS, Nonterminal, was not found in name map.)
(Residue 352: ASP, Nonterminal, was not found in name map.)
(Residue 353: VAL, Nonterminal, was not found in name map.)
(Residue 354: GLU, Nonterminal, was not found in name map.)
(Residue 355: ILE, Nonterminal, was not found in name map.)
(Residue 356: ASN, Nonterminal, was not found in name map.)
(Residue 357: GLY, Nonterminal, was not found in name map.)
(Residue 358: MET, Nonterminal, was not found in name map.)
(Residue 359: PHE, Nonterminal, was not found in name map.)
(Residue 360: ILE, Nonterminal, was not found in name map.)
(Residue 361: PRO, Nonterminal, was not found in name map.)
(Residue 362: LYS, Nonterminal, was not found in name map.)
(Residue 363: GLY, Nonterminal, was not found in name map.)
(Residue 364: VAL, Nonterminal, was not found in name map.)
(Residue 365: VAL, Nonterminal, was not found in name map.)
(Residue 366: VAL, Nonterminal, was not found in name map.)
(Residue 367: MET, Nonterminal, was not found in name map.)
(Residue 368: ILE, Nonterminal, was not found in name map.)
(Residue 369: PRO, Nonterminal, was not found in name map.)
(Residue 370: SER, Nonterminal, was not found in name map.)
(Residue 371: TYR, Nonterminal, was not found in name map.)
(Residue 372: ALA, Nonterminal, was not found in name map.)
(Residue 373: LEU, Nonterminal, was not found in name map.)
(Residue 374: HIE, Nonterminal, was not found in name map.)
(Residue 375: ARG, Nonterminal, was not found in name map.)
(Residue 376: ASP, Nonterminal, was not found in name map.)
(Residue 377: PRO, Nonterminal, was not found in name map.)
(Residue 378: LYS, Nonterminal, was not found in name map.)
(Residue 379: TYR, Nonterminal, was not found in name map.)
(Residue 380: TRP, Nonterminal, was not found in name map.)
(Residue 381: THR, Nonterminal, was not found in name map.)
(Residue 382: GLU, Nonterminal, was not found in name map.)
(Residue 383: PRO, Nonterminal, was not found in name map.)
(Residue 384: GLU, Nonterminal, was not found in name map.)
(Residue 385: LYS, Nonterminal, was not found in name map.)
(Residue 386: PHE, Nonterminal, was not found in name map.)
(Residue 387: LEU, Nonterminal, was not found in name map.)
(Residue 388: PRO, Nonterminal, was not found in name map.)
(Residue 389: GLU, Nonterminal, was not found in name map.)
(Residue 390: ARG, Nonterminal, was not found in name map.)
(Residue 391: PHE, Nonterminal, was not found in name map.)
(Residue 392: SER, Nonterminal, was not found in name map.)
(Residue 393: LYS, Nonterminal, was not found in name map.)
(Residue 394: LYS, Nonterminal, was not found in name map.)
(Residue 395: ASN, Nonterminal, was not found in name map.)
(Residue 396: LYS, Nonterminal, was not found in name map.)
(Residue 397: ASP, Nonterminal, was not found in name map.)
(Residue 398: ASN, Nonterminal, was not found in name map.)
(Residue 399: ILE, Nonterminal, was not found in name map.)
(Residue 400: ASP, Nonterminal, was not found in name map.)
(Residue 401: PRO, Nonterminal, was not found in name map.)
(Residue 402: TYR, Nonterminal, was not found in name map.)
(Residue 403: ILE, Nonterminal, was not found in name map.)
(Residue 404: TYR, Nonterminal, was not found in name map.)
(Residue 405: THR, Nonterminal, was not found in name map.)
(Residue 406: PRO, Nonterminal, was not found in name map.)
(Residue 407: PHE, Nonterminal, was not found in name map.)
(Residue 408: GLY, Nonterminal, was not found in name map.)
(Residue 409: SER, Nonterminal, was not found in name map.)
(Residue 410: GLY, Nonterminal, was not found in name map.)
(Residue 411: PRO, Nonterminal, was not found in name map.)
(Residue 412: ARG, Nonterminal, was not found in name map.)
(Residue 413: ASN, Nonterminal, was not found in name map.)
(Residue 414: CYP, Nonterminal, was not found in name map.)
(Residue 415: ILE, Nonterminal, was not found in name map.)
(Residue 416: GLY, Nonterminal, was not found in name map.)
(Residue 417: MET, Nonterminal, was not found in name map.)
(Residue 418: ARG, Nonterminal, was not found in name map.)
(Residue 419: PHE, Nonterminal, was not found in name map.)
(Residue 420: ALA, Nonterminal, was not found in name map.)
(Residue 421: LEU, Nonterminal, was not found in name map.)
(Residue 422: MET, Nonterminal, was not found in name map.)
(Residue 423: ASN, Nonterminal, was not found in name map.)
(Residue 424: MET, Nonterminal, was not found in name map.)
(Residue 425: LYS, Nonterminal, was not found in name map.)
(Residue 426: LEU, Nonterminal, was not found in name map.)
(Residue 427: ALA, Nonterminal, was not found in name map.)
(Residue 428: LEU, Nonterminal, was not found in name map.)
(Residue 429: ILE, Nonterminal, was not found in name map.)
(Residue 430: ARG, Nonterminal, was not found in name map.)
(Residue 431: VAL, Nonterminal, was not found in name map.)
(Residue 432: LEU, Nonterminal, was not found in name map.)
(Residue 433: GLN, Nonterminal, was not found in name map.)
(Residue 434: ASN, Nonterminal, was not found in name map.)
(Residue 435: PHE, Nonterminal, was not found in name map.)
(Residue 436: SER, Nonterminal, was not found in name map.)
(Residue 437: PHE, Nonterminal, was not found in name map.)
(Residue 438: LYS, Nonterminal, was not found in name map.)
(Residue 439: PRO, Nonterminal, was not found in name map.)
(Residue 440: CYS, Nonterminal, was not found in name map.)
(Residue 441: LYS, Nonterminal, was not found in name map.)
(Residue 442: GLU, Nonterminal, was not found in name map.)
(Residue 443: THR, Nonterminal, was not found in name map.)
(Residue 444: GLN, Nonterminal, was not found in name map.)
(Residue 445: ILE, Nonterminal, was not found in name map.)
(Residue 446: PRO, Nonterminal, was not found in name map.)
(Residue 447: LEU, Nonterminal, was not found in name map.)
(Residue 448: LYS, Nonterminal, was not found in name map.)
(Residue 449: LEU, Nonterminal, was not found in name map.)
(Residue 450: SER, Nonterminal, was not found in name map.)
(Residue 451: LEU, Nonterminal, was not found in name map.)
(Residue 452: GLY, Nonterminal, was not found in name map.)
(Residue 453: GLY, Nonterminal, was not found in name map.)
(Residue 454: LEU, Nonterminal, was not found in name map.)
(Residue 455: LEU, Nonterminal, was not found in name map.)
(Residue 456: GLN, Nonterminal, was not found in name map.)
(Residue 457: PRO, Nonterminal, was not found in name map.)
(Residue 458: GLU, Nonterminal, was not found in name map.)
(Residue 459: LYS, Nonterminal, was not found in name map.)
(Residue 460: PRO, Nonterminal, was not found in name map.)
(Residue 461: VAL, Nonterminal, was not found in name map.)
(Residue 462: VAL, Nonterminal, was not found in name map.)
(Residue 463: LEU, Nonterminal, was not found in name map.)
(Residue 464: LYS, Nonterminal, was not found in name map.)
(Residue 465: VAL, Nonterminal, was not found in name map.)
(Residue 466: GLU, Nonterminal, was not found in name map.)
(Residue 467: SER, Nonterminal, was not found in name map.)
(Residue 468: ARG, Nonterminal, was not found in name map.)
(Residue 469: ASP, Nonterminal, was not found in name map.)
(Residue 470: GLY, Nonterminal, was not found in name map.)
Mapped residue THR, term: Terminal/last, seq. number: 471 to: CTHR.
(Residue 472: HEM, Terminal/last, was not found in name map.)
(Residue 473: OHT, Terminal/last, was not found in name map.)
Joining NHIE - SER
Joining SER - HIE
Joining HIE - GLY
Joining GLY - LEU
Joining LEU - PHE
Joining PHE - LYS
Joining LYS - LYS
Joining LYS - LEU
Joining LEU - GLY
Joining GLY - ILE
Joining ILE - PRO
Joining PRO - GLY
Joining GLY - PRO
Joining PRO - THR
Joining THR - PRO
Joining PRO - LEU
Joining LEU - PRO
Joining PRO - PHE
Joining PHE - LEU
Joining LEU - GLY
Joining GLY - ASN
Joining ASN - ILE
Joining ILE - LEU
Joining LEU - SER
Joining SER - TYR
Joining TYR - HID
Joining HID - LYS
Joining LYS - GLY
Joining GLY - PHE
Joining PHE - CYS
Joining CYS - MET
Joining MET - PHE
Joining PHE - ASP
Joining ASP - MET
Joining MET - GLU
Joining GLU - CYS
Joining CYS - HIE
Joining HIE - LYS
Joining LYS - LYS
Joining LYS - TYR
Joining TYR - GLY
Joining GLY - LYS
Joining LYS - VAL
Joining VAL - TRP
Joining TRP - GLY
Joining GLY - PHE
Joining PHE - TYR
Joining TYR - ASP
Joining ASP - GLY
Joining GLY - GLN
Joining GLN - GLN
Joining GLN - PRO
Joining PRO - VAL
Joining VAL - LEU
Joining LEU - ALA
Joining ALA - ILE
Joining ILE - THR
Joining THR - ASP
Joining ASP - PRO
Joining PRO - ASP
Joining ASP - MET
Joining MET - ILE
Joining ILE - LYS
Joining LYS - THR
Joining THR - VAL
Joining VAL - LEU
Joining LEU - VAL
Joining VAL - LYS
Joining LYS - GLU
Joining GLU - CYS
Joining CYS - TYR
Joining TYR - SER
Joining SER - VAL
Joining VAL - PHE
Joining PHE - THR
Joining THR - ASN
Joining ASN - ARG
Joining ARG - ARG
Joining ARG - PRO
Joining PRO - PHE
Joining PHE - GLY
Joining GLY - PRO
Joining PRO - VAL
Joining VAL - GLY
Joining GLY - PHE
Joining PHE - MET
Joining MET - LYS
Joining LYS - SER
Joining SER - ALA
Joining ALA - ILE
Joining ILE - SER
Joining SER - ILE
Joining ILE - ALA
Joining ALA - GLU
Joining GLU - ASP
Joining ASP - GLU
Joining GLU - GLU
Joining GLU - TRP
Joining TRP - LYS
Joining LYS - ARG
Joining ARG - LEU
Joining LEU - ARG
Joining ARG - SER
Joining SER - LEU
Joining LEU - LEU
Joining LEU - SER
Joining SER - PRO
Joining PRO - THR
Joining THR - PHE
Joining PHE - THR
Joining THR - SER
Joining SER - GLY
Joining GLY - LYS
Joining LYS - LEU
Joining LEU - LYS
Joining LYS - GLU
Joining GLU - MET
Joining MET - VAL
Joining VAL - PRO
Joining PRO - ILE
Joining ILE - ILE
Joining ILE - ALA
Joining ALA - GLN
Joining GLN - TYR
Joining TYR - GLY
Joining GLY - ASP
Joining ASP - VAL
Joining VAL - LEU
Joining LEU - VAL
Joining VAL - ARG
Joining ARG - ASN
Joining ASN - LEU
Joining LEU - ARG
Joining ARG - ARG
Joining ARG - GLU
Joining GLU - ALA
Joining ALA - GLU
Joining GLU - THR
Joining THR - GLY
Joining GLY - LYS
Joining LYS - PRO
Joining PRO - VAL
Joining VAL - THR
Joining THR - LEU
Joining LEU - LYS
Joining LYS - ASP
Joining ASP - VAL
Joining VAL - PHE
Joining PHE - GLY
Joining GLY - ALA
Joining ALA - TYR
Joining TYR - SER
Joining SER - MET
Joining MET - ASP
Joining ASP - VAL
Joining VAL - ILE
Joining ILE - THR
Joining THR - SER
Joining SER - THR
Joining THR - SER
Joining SER - PHE
Joining PHE - GLY
Joining GLY - VAL
Joining VAL - ASN
Joining ASN - ILE
Joining ILE - ASP
Joining ASP - SER
Joining SER - LEU
Joining LEU - ASN
Joining ASN - ASN
Joining ASN - PRO
Joining PRO - GLN
Joining GLN - ASP
Joining ASP - PRO
Joining PRO - PHE
Joining PHE - VAL
Joining VAL - GLU
Joining GLU - ASN
Joining ASN - THR
Joining THR - LYS
Joining LYS - LYS
Joining LYS - LEU
Joining LEU - LEU
Joining LEU - ARG
Joining ARG - PHE
Joining PHE - ASP
Joining ASP - PHE
Joining PHE - LEU
Joining LEU - ASP
Joining ASP - PRO
Joining PRO - PHE
Joining PHE - PHE
Joining PHE - LEU
Joining LEU - SER
Joining SER - ILE
Joining ILE - THR
Joining THR - VAL
Joining VAL - PHE
Joining PHE - PRO
Joining PRO - PHE
Joining PHE - LEU
Joining LEU - ILE
Joining ILE - PRO
Joining PRO - ILE
Joining ILE - LEU
Joining LEU - GLU
Joining GLU - VAL
Joining VAL - LEU
Joining LEU - ASN
Joining ASN - ILE
Joining ILE - CYS
Joining CYS - VAL
Joining VAL - PHE
Joining PHE - PRO
Joining PRO - ARG
Joining ARG - GLU
Joining GLU - VAL
Joining VAL - THR
Joining THR - ASN
Joining ASN - PHE
Joining PHE - LEU
Joining LEU - ARG
Joining ARG - LYS
Joining LYS - SER
Joining SER - VAL
Joining VAL - LYS
Joining LYS - ARG
Joining ARG - MET
Joining MET - LYS
Joining LYS - GLU
Joining GLU - SER
Joining SER - ARG
Joining ARG - LEU
Joining LEU - GLU
Joining GLU - ASP
Joining ASP - THR
Joining THR - GLN
Joining GLN - LYS
Joining LYS - HIE
Joining HIE - ARG
Joining ARG - VAL
Joining VAL - ASP
Joining ASP - PHE
Joining PHE - LEU
Joining LEU - GLN
Joining GLN - LEU
Joining LEU - MET
Joining MET - ILE
Joining ILE - ASP
Joining ASP - SER
Joining SER - GLN
Joining GLN - ASN
Joining ASN - SER
Joining SER - LYS
Joining LYS - GLU
Joining GLU - THR
Joining THR - GLU
Joining GLU - SER
Joining SER - HIE
Joining HIE - LYS
Joining LYS - ALA
Joining ALA - LEU
Joining LEU - SER
Joining SER - ASP
Joining ASP - LEU
Joining LEU - GLU
Joining GLU - LEU
Joining LEU - VAL
Joining VAL - ALA
Joining ALA - GLN
Joining GLN - SER
Joining SER - ILE
Joining ILE - ILE
Joining ILE - PHE
Joining PHE - ILE
Joining ILE - PHE
Joining PHE - ALA
Joining ALA - GLY
Joining GLY - TYR
Joining TYR - GLU
Joining GLU - THR
Joining THR - THR
Joining THR - SER
Joining SER - SER
Joining SER - VAL
Joining VAL - LEU
Joining LEU - SER
Joining SER - PHE
Joining PHE - ILE
Joining ILE - MET
Joining MET - TYR
Joining TYR - GLU
Joining GLU - LEU
Joining LEU - ALA
Joining ALA - THR
Joining THR - HIE
Joining HIE - PRO
Joining PRO - ASP
Joining ASP - VAL
Joining VAL - GLN
Joining GLN - GLN
Joining GLN - LYS
Joining LYS - LEU
Joining LEU - GLN
Joining GLN - GLU
Joining GLU - GLU
Joining GLU - ILE
Joining ILE - ASP
Joining ASP - ALA
Joining ALA - VAL
Joining VAL - LEU
Joining LEU - PRO
Joining PRO - ASN
Joining ASN - LYS
Joining LYS - ALA
Joining ALA - PRO
Joining PRO - PRO
Joining PRO - THR
Joining THR - TYR
Joining TYR - ASP
Joining ASP - THR
Joining THR - VAL
Joining VAL - LEU
Joining LEU - GLN
Joining GLN - MET
Joining MET - GLU
Joining GLU - TYR
Joining TYR - LEU
Joining LEU - ASP
Joining ASP - MET
Joining MET - VAL
Joining VAL - VAL
Joining VAL - ASN
Joining ASN - GLU
Joining GLU - THR
Joining THR - LEU
Joining LEU - ARG
Joining ARG - LEU
Joining LEU - PHE
Joining PHE - PRO
Joining PRO - ILE
Joining ILE - ALA
Joining ALA - MET
Joining MET - ARG
Joining ARG - LEU
Joining LEU - GLU
Joining GLU - ARG
Joining ARG - VAL
Joining VAL - CYS
Joining CYS - LYS
Joining LYS - LYS
Joining LYS - ASP
Joining ASP - VAL
Joining VAL - GLU
Joining GLU - ILE
Joining ILE - ASN
Joining ASN - GLY
Joining GLY - MET
Joining MET - PHE
Joining PHE - ILE
Joining ILE - PRO
Joining PRO - LYS
Joining LYS - GLY
Joining GLY - VAL
Joining VAL - VAL
Joining VAL - VAL
Joining VAL - MET
Joining MET - ILE
Joining ILE - PRO
Joining PRO - SER
Joining SER - TYR
Joining TYR - ALA
Joining ALA - LEU
Joining LEU - HIE
Joining HIE - ARG
Joining ARG - ASP
Joining ASP - PRO
Joining PRO - LYS
Joining LYS - TYR
Joining TYR - TRP
Joining TRP - THR
Joining THR - GLU
Joining GLU - PRO
Joining PRO - GLU
Joining GLU - LYS
Joining LYS - PHE
Joining PHE - LEU
Joining LEU - PRO
Joining PRO - GLU
Joining GLU - ARG
Joining ARG - PHE
Joining PHE - SER
Joining SER - LYS
Joining LYS - LYS
Joining LYS - ASN
Joining ASN - LYS
Joining LYS - ASP
Joining ASP - ASN
Joining ASN - ILE
Joining ILE - ASP
Joining ASP - PRO
Joining PRO - TYR
Joining TYR - ILE
Joining ILE - TYR
Joining TYR - THR
Joining THR - PRO
Joining PRO - PHE
Joining PHE - GLY
Joining GLY - SER
Joining SER - GLY
Joining GLY - PRO
Joining PRO - ARG
Joining ARG - ASN
Joining ASN - CYS
Joining CYS - ILE
Joining ILE - GLY
Joining GLY - MET
Joining MET - ARG
Joining ARG - PHE
Joining PHE - ALA
Joining ALA - LEU
Joining LEU - MET
Joining MET - ASN
Joining ASN - MET
Joining MET - LYS
Joining LYS - LEU
Joining LEU - ALA
Joining ALA - LEU
Joining LEU - ILE
Joining ILE - ARG
Joining ARG - VAL
Joining VAL - LEU
Joining LEU - GLN
Joining GLN - ASN
Joining ASN - PHE
Joining PHE - SER
Joining SER - PHE
Joining PHE - LYS
Joining LYS - PRO
Joining PRO - CYS
Joining CYS - LYS
Joining LYS - GLU
Joining GLU - THR
Joining THR - GLN
Joining GLN - ILE
Joining ILE - PRO
Joining PRO - LEU
Joining LEU - LYS
Joining LYS - LEU
Joining LEU - SER
Joining SER - LEU
Joining LEU - GLY
Joining GLY - GLY
Joining GLY - LEU
Joining LEU - LEU
Joining LEU - GLN
Joining GLN - PRO
Joining PRO - GLU
Joining GLU - LYS
Joining LYS - PRO
Joining PRO - VAL
Joining VAL - VAL
Joining VAL - LEU
Joining LEU - LYS
Joining LYS - VAL
Joining VAL - GLU
Joining GLU - SER
Joining SER - ARG
Joining ARG - ASP
Joining ASP - GLY
Joining GLY - CTHR
  total atoms in file: 3896
  Leap added 3916 missing atoms according to residue templates:
       3886 H / lone pairs
       30 unknown element
> 
> bond aa.415.SG aa.473.FE
> 
> saveamberparm aa b13_invacuo.topo b13_invacuo.coords
Checking Unit.
WARNING: The unperturbed charge of the unit: 3.000400 is not zero.

 -- ignoring the warning.

Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 ** Warning: No sp2 improper torsion term for  C*-CN-CB-CA
        atoms are: CG CE2 CD2 CE3
 ** Warning: No sp2 improper torsion term for  NA-CA-CN-CB
        atoms are: NE1 CZ2 CE2 CD2
 ** Warning: No sp2 improper torsion term for  C*-CN-CB-CA
        atoms are: CG CE2 CD2 CE3
 ** Warning: No sp2 improper torsion term for  NA-CA-CN-CB
        atoms are: NE1 CZ2 CE2 CD2
 ** Warning: No sp2 improper torsion term for  C*-CN-CB-CA
        atoms are: CG CE2 CD2 CE3
 ** Warning: No sp2 improper torsion term for  NA-CA-CN-CB
        atoms are: NE1 CZ2 CE2 CD2
 total 1520 improper torsions applied
Building H-Bond parameters.
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

	CTHR	1
	HEM	1
	NHIE	1
	OHT	1
  )
 (no restraints)
> 
> solvateoct aa TIP3PBOX 12.0 iso
Scaling up box by a factor of 1.302788 to meet diagonal cut criterion
  Solute vdw bounding box:              46.864 77.718 63.235
  Total bounding box for atom centers:  108.985 108.985 108.985
      (box expansion for 'iso' is  60.9%)
  Solvent unit box:                     18.774 18.774 18.774
The number of boxes:  x= 6  y= 6  z= 6
Adding box at: x=0  y=0  z=0
Center of solvent box is: 46.935873, 46.935873, 46.935873
Adding box at: x=0  y=0  z=1
Center of solvent box is: 46.935873, 46.935873, 28.161524
Adding box at: x=0  y=0  z=2
Center of solvent box is: 46.935873, 46.935873, 9.387175
Adding box at: x=0  y=0  z=3
Center of solvent box is: 46.935873, 46.935873, -9.387175
Adding box at: x=0  y=0  z=4
Center of solvent box is: 46.935873, 46.935873, -28.161524
Adding box at: x=0  y=0  z=5
Center of solvent box is: 46.935873, 46.935873, -46.935873
Adding box at: x=0  y=1  z=0
Center of solvent box is: 46.935873, 28.161524, 46.935873
Adding box at: x=0  y=1  z=1
Center of solvent box is: 46.935873, 28.161524, 28.161524
Adding box at: x=0  y=1  z=2
Center of solvent box is: 46.935873, 28.161524, 9.387175
Adding box at: x=0  y=1  z=3
Center of solvent box is: 46.935873, 28.161524, -9.387175
Adding box at: x=0  y=1  z=4
Center of solvent box is: 46.935873, 28.161524, -28.161524
Adding box at: x=0  y=1  z=5
Center of solvent box is: 46.935873, 28.161524, -46.935873
Adding box at: x=0  y=2  z=0
Center of solvent box is: 46.935873, 9.387175, 46.935873
Adding box at: x=0  y=2  z=1
Center of solvent box is: 46.935873, 9.387175, 28.161524
Adding box at: x=0  y=2  z=2
Center of solvent box is: 46.935873, 9.387175, 9.387175
Adding box at: x=0  y=2  z=3
Center of solvent box is: 46.935873, 9.387175, -9.387175
Adding box at: x=0  y=2  z=4
Center of solvent box is: 46.935873, 9.387175, -28.161524
Adding box at: x=0  y=2  z=5
Center of solvent box is: 46.935873, 9.387175, -46.935873
Adding box at: x=0  y=3  z=0
Center of solvent box is: 46.935873, -9.387175, 46.935873
Adding box at: x=0  y=3  z=1
Center of solvent box is: 46.935873, -9.387175, 28.161524
Adding box at: x=0  y=3  z=2
Center of solvent box is: 46.935873, -9.387175, 9.387175
Adding box at: x=0  y=3  z=3
Center of solvent box is: 46.935873, -9.387175, -9.387175
Adding box at: x=0  y=3  z=4
Center of solvent box is: 46.935873, -9.387175, -28.161524
Adding box at: x=0  y=3  z=5
Center of solvent box is: 46.935873, -9.387175, -46.935873
Adding box at: x=0  y=4  z=0
Center of solvent box is: 46.935873, -28.161524, 46.935873
Adding box at: x=0  y=4  z=1
Center of solvent box is: 46.935873, -28.161524, 28.161524
Adding box at: x=0  y=4  z=2
Center of solvent box is: 46.935873, -28.161524, 9.387175
Adding box at: x=0  y=4  z=3
Center of solvent box is: 46.935873, -28.161524, -9.387175
Adding box at: x=0  y=4  z=4
Center of solvent box is: 46.935873, -28.161524, -28.161524
Adding box at: x=0  y=4  z=5
Center of solvent box is: 46.935873, -28.161524, -46.935873
Adding box at: x=0  y=5  z=0
Center of solvent box is: 46.935873, -46.935873, 46.935873
Adding box at: x=0  y=5  z=1
Center of solvent box is: 46.935873, -46.935873, 28.161524
Adding box at: x=0  y=5  z=2
Center of solvent box is: 46.935873, -46.935873, 9.387175
Adding box at: x=0  y=5  z=3
Center of solvent box is: 46.935873, -46.935873, -9.387175
Adding box at: x=0  y=5  z=4
Center of solvent box is: 46.935873, -46.935873, -28.161524
Adding box at: x=0  y=5  z=5
Center of solvent box is: 46.935873, -46.935873, -46.935873
Adding box at: x=1  y=0  z=0
Center of solvent box is: 28.161524, 46.935873, 46.935873
Adding box at: x=1  y=0  z=1
Center of solvent box is: 28.161524, 46.935873, 28.161524
Adding box at: x=1  y=0  z=2
Center of solvent box is: 28.161524, 46.935873, 9.387175
Adding box at: x=1  y=0  z=3
Center of solvent box is: 28.161524, 46.935873, -9.387175
Adding box at: x=1  y=0  z=4
Center of solvent box is: 28.161524, 46.935873, -28.161524
Adding box at: x=1  y=0  z=5
Center of solvent box is: 28.161524, 46.935873, -46.935873
Adding box at: x=1  y=1  z=0
Center of solvent box is: 28.161524, 28.161524, 46.935873
Adding box at: x=1  y=1  z=1
Center of solvent box is: 28.161524, 28.161524, 28.161524
Adding box at: x=1  y=1  z=2
Center of solvent box is: 28.161524, 28.161524, 9.387175
Adding box at: x=1  y=1  z=3
Center of solvent box is: 28.161524, 28.161524, -9.387175
Adding box at: x=1  y=1  z=4
Center of solvent box is: 28.161524, 28.161524, -28.161524
Adding box at: x=1  y=1  z=5
Center of solvent box is: 28.161524, 28.161524, -46.935873
Adding box at: x=1  y=2  z=0
Center of solvent box is: 28.161524, 9.387175, 46.935873
Adding box at: x=1  y=2  z=1
Center of solvent box is: 28.161524, 9.387175, 28.161524
Adding box at: x=1  y=2  z=2
Center of solvent box is: 28.161524, 9.387175, 9.387175
Adding box at: x=1  y=2  z=3
Center of solvent box is: 28.161524, 9.387175, -9.387175
Adding box at: x=1  y=2  z=4
Center of solvent box is: 28.161524, 9.387175, -28.161524
Adding box at: x=1  y=2  z=5
Center of solvent box is: 28.161524, 9.387175, -46.935873
Adding box at: x=1  y=3  z=0
Center of solvent box is: 28.161524, -9.387175, 46.935873
Adding box at: x=1  y=3  z=1
Center of solvent box is: 28.161524, -9.387175, 28.161524
Adding box at: x=1  y=3  z=2
Center of solvent box is: 28.161524, -9.387175, 9.387175
Adding box at: x=1  y=3  z=3
Center of solvent box is: 28.161524, -9.387175, -9.387175
Adding box at: x=1  y=3  z=4
Center of solvent box is: 28.161524, -9.387175, -28.161524
Adding box at: x=1  y=3  z=5
Center of solvent box is: 28.161524, -9.387175, -46.935873
Adding box at: x=1  y=4  z=0
Center of solvent box is: 28.161524, -28.161524, 46.935873
Adding box at: x=1  y=4  z=1
Center of solvent box is: 28.161524, -28.161524, 28.161524
Adding box at: x=1  y=4  z=2
Center of solvent box is: 28.161524, -28.161524, 9.387175
Adding box at: x=1  y=4  z=3
Center of solvent box is: 28.161524, -28.161524, -9.387175
Adding box at: x=1  y=4  z=4
Center of solvent box is: 28.161524, -28.161524, -28.161524
Adding box at: x=1  y=4  z=5
Center of solvent box is: 28.161524, -28.161524, -46.935873
Adding box at: x=1  y=5  z=0
Center of solvent box is: 28.161524, -46.935873, 46.935873
Adding box at: x=1  y=5  z=1
Center of solvent box is: 28.161524, -46.935873, 28.161524
Adding box at: x=1  y=5  z=2
Center of solvent box is: 28.161524, -46.935873, 9.387175
Adding box at: x=1  y=5  z=3
Center of solvent box is: 28.161524, -46.935873, -9.387175
Adding box at: x=1  y=5  z=4
Center of solvent box is: 28.161524, -46.935873, -28.161524
Adding box at: x=1  y=5  z=5
Center of solvent box is: 28.161524, -46.935873, -46.935873
Adding box at: x=2  y=0  z=0
Center of solvent box is: 9.387175, 46.935873, 46.935873
Adding box at: x=2  y=0  z=1
Center of solvent box is: 9.387175, 46.935873, 28.161524
Adding box at: x=2  y=0  z=2
Center of solvent box is: 9.387175, 46.935873, 9.387175
Adding box at: x=2  y=0  z=3
Center of solvent box is: 9.387175, 46.935873, -9.387175
Adding box at: x=2  y=0  z=4
Center of solvent box is: 9.387175, 46.935873, -28.161524
Adding box at: x=2  y=0  z=5
Center of solvent box is: 9.387175, 46.935873, -46.935873
Adding box at: x=2  y=1  z=0
Center of solvent box is: 9.387175, 28.161524, 46.935873
Adding box at: x=2  y=1  z=1
Center of solvent box is: 9.387175, 28.161524, 28.161524
Adding box at: x=2  y=1  z=2
Center of solvent box is: 9.387175, 28.161524, 9.387175
Adding box at: x=2  y=1  z=3
Center of solvent box is: 9.387175, 28.161524, -9.387175
Adding box at: x=2  y=1  z=4
Center of solvent box is: 9.387175, 28.161524, -28.161524
Adding box at: x=2  y=1  z=5
Center of solvent box is: 9.387175, 28.161524, -46.935873
Adding box at: x=2  y=2  z=0
Center of solvent box is: 9.387175, 9.387175, 46.935873
Adding box at: x=2  y=2  z=1
Center of solvent box is: 9.387175, 9.387175, 28.161524
Adding box at: x=2  y=2  z=2
Center of solvent box is: 9.387175, 9.387175, 9.387175
Adding box at: x=2  y=2  z=3
Center of solvent box is: 9.387175, 9.387175, -9.387175
Adding box at: x=2  y=2  z=4
Center of solvent box is: 9.387175, 9.387175, -28.161524
Adding box at: x=2  y=2  z=5
Center of solvent box is: 9.387175, 9.387175, -46.935873
Adding box at: x=2  y=3  z=0
Center of solvent box is: 9.387175, -9.387175, 46.935873
Adding box at: x=2  y=3  z=1
Center of solvent box is: 9.387175, -9.387175, 28.161524
Adding box at: x=2  y=3  z=2
Center of solvent box is: 9.387175, -9.387175, 9.387175
Adding box at: x=2  y=3  z=3
Center of solvent box is: 9.387175, -9.387175, -9.387175
Adding box at: x=2  y=3  z=4
Center of solvent box is: 9.387175, -9.387175, -28.161524
Adding box at: x=2  y=3  z=5
Center of solvent box is: 9.387175, -9.387175, -46.935873
Adding box at: x=2  y=4  z=0
Center of solvent box is: 9.387175, -28.161524, 46.935873
Adding box at: x=2  y=4  z=1
Center of solvent box is: 9.387175, -28.161524, 28.161524
Adding box at: x=2  y=4  z=2
Center of solvent box is: 9.387175, -28.161524, 9.387175
Adding box at: x=2  y=4  z=3
Center of solvent box is: 9.387175, -28.161524, -9.387175
Adding box at: x=2  y=4  z=4
Center of solvent box is: 9.387175, -28.161524, -28.161524
Adding box at: x=2  y=4  z=5
Center of solvent box is: 9.387175, -28.161524, -46.935873
Adding box at: x=2  y=5  z=0
Center of solvent box is: 9.387175, -46.935873, 46.935873
Adding box at: x=2  y=5  z=1
Center of solvent box is: 9.387175, -46.935873, 28.161524
Adding box at: x=2  y=5  z=2
Center of solvent box is: 9.387175, -46.935873, 9.387175
Adding box at: x=2  y=5  z=3
Center of solvent box is: 9.387175, -46.935873, -9.387175
Adding box at: x=2  y=5  z=4
Center of solvent box is: 9.387175, -46.935873, -28.161524
Adding box at: x=2  y=5  z=5
Center of solvent box is: 9.387175, -46.935873, -46.935873
Adding box at: x=3  y=0  z=0
Center of solvent box is: -9.387175, 46.935873, 46.935873
Adding box at: x=3  y=0  z=1
Center of solvent box is: -9.387175, 46.935873, 28.161524
Adding box at: x=3  y=0  z=2
Center of solvent box is: -9.387175, 46.935873, 9.387175
Adding box at: x=3  y=0  z=3
Center of solvent box is: -9.387175, 46.935873, -9.387175
Adding box at: x=3  y=0  z=4
Center of solvent box is: -9.387175, 46.935873, -28.161524
Adding box at: x=3  y=0  z=5
Center of solvent box is: -9.387175, 46.935873, -46.935873
Adding box at: x=3  y=1  z=0
Center of solvent box is: -9.387175, 28.161524, 46.935873
Adding box at: x=3  y=1  z=1
Center of solvent box is: -9.387175, 28.161524, 28.161524
Adding box at: x=3  y=1  z=2
Center of solvent box is: -9.387175, 28.161524, 9.387175
Adding box at: x=3  y=1  z=3
Center of solvent box is: -9.387175, 28.161524, -9.387175
Adding box at: x=3  y=1  z=4
Center of solvent box is: -9.387175, 28.161524, -28.161524
Adding box at: x=3  y=1  z=5
Center of solvent box is: -9.387175, 28.161524, -46.935873
Adding box at: x=3  y=2  z=0
Center of solvent box is: -9.387175, 9.387175, 46.935873
Adding box at: x=3  y=2  z=1
Center of solvent box is: -9.387175, 9.387175, 28.161524
Adding box at: x=3  y=2  z=2
Center of solvent box is: -9.387175, 9.387175, 9.387175
Adding box at: x=3  y=2  z=3
Center of solvent box is: -9.387175, 9.387175, -9.387175
Adding box at: x=3  y=2  z=4
Center of solvent box is: -9.387175, 9.387175, -28.161524
Adding box at: x=3  y=2  z=5
Center of solvent box is: -9.387175, 9.387175, -46.935873
Adding box at: x=3  y=3  z=0
Center of solvent box is: -9.387175, -9.387175, 46.935873
Adding box at: x=3  y=3  z=1
Center of solvent box is: -9.387175, -9.387175, 28.161524
Adding box at: x=3  y=3  z=2
Center of solvent box is: -9.387175, -9.387175, 9.387175
Adding box at: x=3  y=3  z=3
Center of solvent box is: -9.387175, -9.387175, -9.387175
Adding box at: x=3  y=3  z=4
Center of solvent box is: -9.387175, -9.387175, -28.161524
Adding box at: x=3  y=3  z=5
Center of solvent box is: -9.387175, -9.387175, -46.935873
Adding box at: x=3  y=4  z=0
Center of solvent box is: -9.387175, -28.161524, 46.935873
Adding box at: x=3  y=4  z=1
Center of solvent box is: -9.387175, -28.161524, 28.161524
Adding box at: x=3  y=4  z=2
Center of solvent box is: -9.387175, -28.161524, 9.387175
Adding box at: x=3  y=4  z=3
Center of solvent box is: -9.387175, -28.161524, -9.387175
Adding box at: x=3  y=4  z=4
Center of solvent box is: -9.387175, -28.161524, -28.161524
Adding box at: x=3  y=4  z=5
Center of solvent box is: -9.387175, -28.161524, -46.935873
Adding box at: x=3  y=5  z=0
Center of solvent box is: -9.387175, -46.935873, 46.935873
Adding box at: x=3  y=5  z=1
Center of solvent box is: -9.387175, -46.935873, 28.161524
Adding box at: x=3  y=5  z=2
Center of solvent box is: -9.387175, -46.935873, 9.387175
Adding box at: x=3  y=5  z=3
Center of solvent box is: -9.387175, -46.935873, -9.387175
Adding box at: x=3  y=5  z=4
Center of solvent box is: -9.387175, -46.935873, -28.161524
Adding box at: x=3  y=5  z=5
Center of solvent box is: -9.387175, -46.935873, -46.935873
Adding box at: x=4  y=0  z=0
Center of solvent box is: -28.161524, 46.935873, 46.935873
Adding box at: x=4  y=0  z=1
Center of solvent box is: -28.161524, 46.935873, 28.161524
Adding box at: x=4  y=0  z=2
Center of solvent box is: -28.161524, 46.935873, 9.387175
Adding box at: x=4  y=0  z=3
Center of solvent box is: -28.161524, 46.935873, -9.387175
Adding box at: x=4  y=0  z=4
Center of solvent box is: -28.161524, 46.935873, -28.161524
Adding box at: x=4  y=0  z=5
Center of solvent box is: -28.161524, 46.935873, -46.935873
Adding box at: x=4  y=1  z=0
Center of solvent box is: -28.161524, 28.161524, 46.935873
Adding box at: x=4  y=1  z=1
Center of solvent box is: -28.161524, 28.161524, 28.161524
Adding box at: x=4  y=1  z=2
Center of solvent box is: -28.161524, 28.161524, 9.387175
Adding box at: x=4  y=1  z=3
Center of solvent box is: -28.161524, 28.161524, -9.387175
Adding box at: x=4  y=1  z=4
Center of solvent box is: -28.161524, 28.161524, -28.161524
Adding box at: x=4  y=1  z=5
Center of solvent box is: -28.161524, 28.161524, -46.935873
Adding box at: x=4  y=2  z=0
Center of solvent box is: -28.161524, 9.387175, 46.935873
Adding box at: x=4  y=2  z=1
Center of solvent box is: -28.161524, 9.387175, 28.161524
Adding box at: x=4  y=2  z=2
Center of solvent box is: -28.161524, 9.387175, 9.387175
Adding box at: x=4  y=2  z=3
Center of solvent box is: -28.161524, 9.387175, -9.387175
Adding box at: x=4  y=2  z=4
Center of solvent box is: -28.161524, 9.387175, -28.161524
Adding box at: x=4  y=2  z=5
Center of solvent box is: -28.161524, 9.387175, -46.935873
Adding box at: x=4  y=3  z=0
Center of solvent box is: -28.161524, -9.387175, 46.935873
Adding box at: x=4  y=3  z=1
Center of solvent box is: -28.161524, -9.387175, 28.161524
Adding box at: x=4  y=3  z=2
Center of solvent box is: -28.161524, -9.387175, 9.387175
Adding box at: x=4  y=3  z=3
Center of solvent box is: -28.161524, -9.387175, -9.387175
Adding box at: x=4  y=3  z=4
Center of solvent box is: -28.161524, -9.387175, -28.161524
Adding box at: x=4  y=3  z=5
Center of solvent box is: -28.161524, -9.387175, -46.935873
Adding box at: x=4  y=4  z=0
Center of solvent box is: -28.161524, -28.161524, 46.935873
Adding box at: x=4  y=4  z=1
Center of solvent box is: -28.161524, -28.161524, 28.161524
Adding box at: x=4  y=4  z=2
Center of solvent box is: -28.161524, -28.161524, 9.387175
Adding box at: x=4  y=4  z=3
Center of solvent box is: -28.161524, -28.161524, -9.387175
Adding box at: x=4  y=4  z=4
Center of solvent box is: -28.161524, -28.161524, -28.161524
Adding box at: x=4  y=4  z=5
Center of solvent box is: -28.161524, -28.161524, -46.935873
Adding box at: x=4  y=5  z=0
Center of solvent box is: -28.161524, -46.935873, 46.935873
Adding box at: x=4  y=5  z=1
Center of solvent box is: -28.161524, -46.935873, 28.161524
Adding box at: x=4  y=5  z=2
Center of solvent box is: -28.161524, -46.935873, 9.387175
Adding box at: x=4  y=5  z=3
Center of solvent box is: -28.161524, -46.935873, -9.387175
Adding box at: x=4  y=5  z=4
Center of solvent box is: -28.161524, -46.935873, -28.161524
Adding box at: x=4  y=5  z=5
Center of solvent box is: -28.161524, -46.935873, -46.935873
Adding box at: x=5  y=0  z=0
Center of solvent box is: -46.935873, 46.935873, 46.935873
Adding box at: x=5  y=0  z=1
Center of solvent box is: -46.935873, 46.935873, 28.161524
Adding box at: x=5  y=0  z=2
Center of solvent box is: -46.935873, 46.935873, 9.387175
Adding box at: x=5  y=0  z=3
Center of solvent box is: -46.935873, 46.935873, -9.387175
Adding box at: x=5  y=0  z=4
Center of solvent box is: -46.935873, 46.935873, -28.161524
Adding box at: x=5  y=0  z=5
Center of solvent box is: -46.935873, 46.935873, -46.935873
Adding box at: x=5  y=1  z=0
Center of solvent box is: -46.935873, 28.161524, 46.935873
Adding box at: x=5  y=1  z=1
Center of solvent box is: -46.935873, 28.161524, 28.161524
Adding box at: x=5  y=1  z=2
Center of solvent box is: -46.935873, 28.161524, 9.387175
Adding box at: x=5  y=1  z=3
Center of solvent box is: -46.935873, 28.161524, -9.387175
Adding box at: x=5  y=1  z=4
Center of solvent box is: -46.935873, 28.161524, -28.161524
Adding box at: x=5  y=1  z=5
Center of solvent box is: -46.935873, 28.161524, -46.935873
Adding box at: x=5  y=2  z=0
Center of solvent box is: -46.935873, 9.387175, 46.935873
Adding box at: x=5  y=2  z=1
Center of solvent box is: -46.935873, 9.387175, 28.161524
Adding box at: x=5  y=2  z=2
Center of solvent box is: -46.935873, 9.387175, 9.387175
Adding box at: x=5  y=2  z=3
Center of solvent box is: -46.935873, 9.387175, -9.387175
Adding box at: x=5  y=2  z=4
Center of solvent box is: -46.935873, 9.387175, -28.161524
Adding box at: x=5  y=2  z=5
Center of solvent box is: -46.935873, 9.387175, -46.935873
Adding box at: x=5  y=3  z=0
Center of solvent box is: -46.935873, -9.387175, 46.935873
Adding box at: x=5  y=3  z=1
Center of solvent box is: -46.935873, -9.387175, 28.161524
Adding box at: x=5  y=3  z=2
Center of solvent box is: -46.935873, -9.387175, 9.387175
Adding box at: x=5  y=3  z=3
Center of solvent box is: -46.935873, -9.387175, -9.387175
Adding box at: x=5  y=3  z=4
Center of solvent box is: -46.935873, -9.387175, -28.161524
Adding box at: x=5  y=3  z=5
Center of solvent box is: -46.935873, -9.387175, -46.935873
Adding box at: x=5  y=4  z=0
Center of solvent box is: -46.935873, -28.161524, 46.935873
Adding box at: x=5  y=4  z=1
Center of solvent box is: -46.935873, -28.161524, 28.161524
Adding box at: x=5  y=4  z=2
Center of solvent box is: -46.935873, -28.161524, 9.387175
Adding box at: x=5  y=4  z=3
Center of solvent box is: -46.935873, -28.161524, -9.387175
Adding box at: x=5  y=4  z=4
Center of solvent box is: -46.935873, -28.161524, -28.161524
Adding box at: x=5  y=4  z=5
Center of solvent box is: -46.935873, -28.161524, -46.935873
Adding box at: x=5  y=5  z=0
Center of solvent box is: -46.935873, -46.935873, 46.935873
Adding box at: x=5  y=5  z=1
Center of solvent box is: -46.935873, -46.935873, 28.161524
Adding box at: x=5  y=5  z=2
Center of solvent box is: -46.935873, -46.935873, 9.387175
Adding box at: x=5  y=5  z=3
Center of solvent box is: -46.935873, -46.935873, -9.387175
Adding box at: x=5  y=5  z=4
Center of solvent box is: -46.935873, -46.935873, -28.161524
Adding box at: x=5  y=5  z=5
Center of solvent box is: -46.935873, -46.935873, -46.935873
  Volume: 665230.202 A^3 (oct)
  Total mass 365354.982 amu,  Density 0.912 g/cc
  Added 17225 residues.
> 
> addions aa Cl- 0
3 Cl- ions required to neutralize.
Adding 3 counter ions to "aa" using 1A grid
Total solute charge:   3.00  Max atom radius:   2.00
Grid extends from solute vdw + 2.47  to  8.47
Box:
   enclosing:  -40.26 -42.40 -40.91   39.61 41.57 40.79
   sized:			      87.74 85.60 87.09
   edge:        128.00
Resolution:      1.00 Angstrom.
Tree depth: 7
grid build: 1 sec
Volume =  4.03% of box, grid points 84430
Solvent present: replacing closest with ion
	 when steric overlaps occur
Calculating grid charges
charges: 118 sec
(Replacing solvent molecule)
Placed Cl- in aa at (-22.41, -14.05, -7.10).
(Replacing solvent molecule)
Placed Cl- in aa at (-3.35, 29.80, 6.72).
(Replacing solvent molecule)
Placed Cl- in aa at (31.73, 0.34, 9.04).

Done adding ions.
> 
> addions aa Na+ 10 Cl- 10
Adding 20 counter ions to "aa" using 1A grid
Total solute charge:   0.00  Max atom radius:   2.47
Grid extends from solute vdw + 1.32  to  7.79
Box:
   enclosing:  -39.58 -41.72 -40.23   39.52 40.89 40.11
   sized:			      88.42 86.28 87.77
   edge:        128.00
Resolution:      1.00 Angstrom.
Tree depth: 7
grid build: 1 sec
Volume =  4.38% of box, grid points 91925
Solvent present: replacing closest with ion
	 when steric overlaps occur
Calculating grid charges
charges: 133 sec
(Replacing solvent molecule)
Placed Na+ in aa at (-6.95, -31.92, -0.71).
(Replacing solvent molecule)
Placed Cl- in aa at (9.25, -1.62, 21.41).
(Replacing solvent molecule)
Placed Na+ in aa at (11.92, -4.10, 18.59).
(Replacing solvent molecule)
Placed Cl- in aa at (14.54, -3.32, 15.60).
(Replacing solvent molecule)
Placed Na+ in aa at (15.00, 1.03, 15.22).
(Replacing solvent molecule)
Placed Cl- in aa at (11.36, -4.69, 21.73).
(Replacing solvent molecule)
Placed Na+ in aa at (14.07, -1.15, 21.63).
(Replacing solvent molecule)
Placed Cl- in aa at (13.31, 0.59, 19.65).
(Replacing solvent molecule)
Placed Na+ in aa at (26.03, -4.69, -26.39).
(Replacing solvent molecule)
Placed Cl- in aa at (21.56, -8.66, -22.49).
(Replacing solvent molecule)
Placed Na+ in aa at (13.04, 10.31, 22.98).
(Replacing solvent molecule)
Placed Cl- in aa at (11.26, -20.47, 6.54).
(Replacing solvent molecule)
Placed Na+ in aa at (9.22, -21.57, 4.14).
(Replacing solvent molecule)
Placed Cl- in aa at (3.87, -24.55, 3.08).
(Replacing solvent molecule)
Placed Na+ in aa at (5.52, -24.30, -0.66).
(Replacing solvent molecule)
Placed Cl- in aa at (9.89, -24.45, 1.28).
(Replacing solvent molecule)
Placed Na+ in aa at (5.70, -22.39, 6.63).
(Replacing solvent molecule)
Placed Cl- in aa at (5.45, -24.99, 12.77).
(Replacing solvent molecule)
Placed Na+ in aa at (5.32, -21.37, 14.74).
(Replacing solvent molecule)
Placed Cl- in aa at (6.73, -21.48, 9.77).

Done adding ions.
> addions aa Na+ 10 Cl- 10
Adding 20 counter ions to "aa" using 1A grid
Total solute charge:   0.00  Max atom radius:   2.47
Grid extends from solute vdw + 1.32  to  7.79
Box:
   enclosing:  -39.58 -41.72 -40.23   39.52 40.89 40.11
   sized:			      88.42 86.28 87.77
   edge:        128.00
Resolution:      1.00 Angstrom.
Tree depth: 7
grid build: 2 sec
Volume =  4.44% of box, grid points 93009
Solvent present: replacing closest with ion
	 when steric overlaps occur
Calculating grid charges
charges: 124 sec
(Replacing solvent molecule)
Placed Na+ in aa at (11.49, -24.90, -0.93).
(Replacing solvent molecule)
Placed Cl- in aa at (9.74, -27.46, -4.52).
(Replacing solvent molecule)
Placed Na+ in aa at (10.27, -29.53, -8.17).
(Replacing solvent molecule)
Placed Cl- in aa at (10.99, -33.87, -10.15).
(Replacing solvent molecule)
Placed Na+ in aa at (11.00, -36.92, -12.50).
(Replacing solvent molecule)
Placed Cl- in aa at (9.88, -36.75, -8.32).
(Replacing solvent molecule)
Placed Na+ in aa at (10.08, -29.33, -2.46).
(Replacing solvent molecule)
Placed Cl- in aa at (13.16, -37.38, -16.69).
(Replacing solvent molecule)
Placed Na+ in aa at (-2.31, -27.99, -3.29).
(Replacing solvent molecule)
Placed Cl- in aa at (-21.94, -10.59, -3.04).
(Replacing solvent molecule)
Placed Na+ in aa at (-26.50, -12.12, -4.34).
(Replacing solvent molecule)
Placed Cl- in aa at (-28.05, -9.66, -4.85).
(Replacing solvent molecule)
Placed Na+ in aa at (-30.86, -7.87, -7.56).
(Replacing solvent molecule)
Placed Cl- in aa at (-29.31, -4.61, -9.15).
(Replacing solvent molecule)
Placed Na+ in aa at (-25.62, -0.78, -11.63).
(Replacing solvent molecule)
Placed Cl- in aa at (-27.41, 2.56, -10.29).
(Replacing solvent molecule)
Placed Na+ in aa at (-31.20, 2.60, -10.61).
(Replacing solvent molecule)
Placed Cl- in aa at (7.24, -27.95, -3.27).
(Replacing solvent molecule)
Placed Na+ in aa at (10.82, -32.08, -5.49).
(Replacing solvent molecule)
Placed Cl- in aa at (14.15, -30.12, -0.66).

Done adding ions.
> addions aa Na+ 10 Cl- 10
Adding 20 counter ions to "aa" using 1A grid
Total solute charge:   0.00  Max atom radius:   2.47
Grid extends from solute vdw + 1.32  to  7.79
Box:
   enclosing:  -39.58 -45.17 -40.23   39.52 40.89 40.11
   sized:			      88.42 82.83 87.77
   edge:        128.00
Resolution:      1.00 Angstrom.
Tree depth: 7
grid build: 1 sec
Volume =  4.60% of box, grid points 96441
Solvent present: replacing closest with ion
	 when steric overlaps occur
Calculating grid charges
charges: 142 sec
(Replacing solvent molecule)
Placed Na+ in aa at (-8.74, -26.43, -1.22).
(Replacing solvent molecule)
Placed Cl- in aa at (-9.65, -28.38, 1.20).
(Replacing solvent molecule)
Placed Na+ in aa at (-8.01, -31.36, 4.86).
(Replacing solvent molecule)
Placed Cl- in aa at (-9.45, -33.19, 0.89).
(Replacing solvent molecule)
Placed Na+ in aa at (-11.91, -33.18, -2.67).
(Replacing solvent molecule)
Placed Cl- in aa at (-11.63, -37.99, -4.24).
(Replacing solvent molecule)
Placed Na+ in aa at (-10.32, -35.35, -4.82).
(Replacing solvent molecule)
Placed Cl- in aa at (-14.93, -31.81, -2.83).
(Replacing solvent molecule)
Placed Na+ in aa at (-18.41, -26.70, -0.67).
(Replacing solvent molecule)
Placed Cl- in aa at (-17.24, -25.46, 6.06).
(Replacing solvent molecule)
Placed Na+ in aa at (-13.89, -23.81, 5.46).
(Replacing solvent molecule)
Placed Cl- in aa at (-17.51, -21.97, 1.94).
(Replacing solvent molecule)
Placed Na+ in aa at (-19.76, -20.73, -0.90).
(Replacing solvent molecule)
Placed Cl- in aa at (-23.00, -19.66, -1.81).
(Replacing solvent molecule)
Placed Na+ in aa at (-23.14, -15.24, -4.40).
(Replacing solvent molecule)
Placed Cl- in aa at (-19.42, -19.14, -6.81).
(Replacing solvent molecule)
Placed Na+ in aa at (-22.62, -19.38, -9.82).
(Replacing solvent molecule)
Placed Cl- in aa at (-24.22, -16.95, -10.39).
(Replacing solvent molecule)
Placed Na+ in aa at (-21.11, -12.94, -12.59).
(Replacing solvent molecule)
Placed Cl- in aa at (-21.94, -16.69, -15.47).

Done adding ions.
> addions aa Na+ 10 Cl- 10
Adding 20 counter ions to "aa" using 1A grid
Total solute charge:   0.00  Max atom radius:   2.47
Grid extends from solute vdw + 1.32  to  7.79
Box:
   enclosing:  -39.58 -45.78 -40.23   39.52 40.89 40.11
   sized:			      88.42 82.22 87.77
   edge:        128.00
Resolution:      1.00 Angstrom.
Tree depth: 7
grid build: 1 sec
Volume =  4.70% of box, grid points 98590
Solvent present: replacing closest with ion
	 when steric overlaps occur
Calculating grid charges
charges: 143 sec
(No solvent overlap)
Placed Na+ in aa at (12.42, 17.22, -5.23).
(Replacing solvent molecule)
Placed Cl- in aa at (20.73, 18.94, -23.10).
(Replacing solvent molecule)
Placed Na+ in aa at (20.97, 21.00, -19.67).
(Replacing solvent molecule)
Placed Cl- in aa at (18.63, 22.17, -21.09).
(Replacing solvent molecule)
Placed Na+ in aa at (22.54, 23.15, -22.74).
(Replacing solvent molecule)
Placed Cl- in aa at (23.94, 19.19, -20.08).
(Replacing solvent molecule)
Placed Na+ in aa at (26.78, 10.22, -23.57).
(Replacing solvent molecule)
Placed Cl- in aa at (24.51, 14.63, -21.69).
(Replacing solvent molecule)
Placed Na+ in aa at (24.62, 15.62, -17.90).
(Replacing solvent molecule)
Placed Cl- in aa at (26.37, 12.81, -17.46).
(Replacing solvent molecule)
Placed Na+ in aa at (29.11, 13.15, -20.67).
(Replacing solvent molecule)
Placed Cl- in aa at (30.90, 9.08, -22.41).
(Replacing solvent molecule)
Placed Na+ in aa at (24.86, 16.56, -23.49).
(Replacing solvent molecule)
Placed Cl- in aa at (-0.76, 24.32, -15.73).
(Replacing solvent molecule)
Placed Na+ in aa at (-1.77, 30.14, -14.74).
(Replacing solvent molecule)
Placed Cl- in aa at (-1.62, 32.08, -9.14).
(Replacing solvent molecule)
Placed Na+ in aa at (-1.59, 29.04, -5.15).
(Replacing solvent molecule)
Placed Cl- in aa at (1.83, 28.02, -2.95).
(Replacing solvent molecule)
Placed Na+ in aa at (4.03, 26.71, -1.14).
(Replacing solvent molecule)
Placed Cl- in aa at (2.47, 31.25, -6.90).

Done adding ions.
> addions aa Na+ 10 Cl- 10
Adding 20 counter ions to "aa" using 1A grid
Total solute charge:   0.00  Max atom radius:   2.47
Grid extends from solute vdw + 1.32  to  7.79
Box:
   enclosing:  -39.58 -45.78 -40.23   39.52 40.89 40.11
   sized:			      88.42 82.22 87.77
   edge:        128.00
Resolution:      1.00 Angstrom.
Tree depth: 7
grid build: 1 sec
Volume =  4.82% of box, grid points 101000
Solvent present: replacing closest with ion
	 when steric overlaps occur
Calculating grid charges
charges: 149 sec
(Replacing solvent molecule)
Placed Na+ in aa at (-6.15, 12.81, 35.64).
(Replacing solvent molecule)
Placed Cl- in aa at (-5.30, 16.40, 34.07).
(Replacing solvent molecule)
Placed Na+ in aa at (-0.80, 13.56, 34.87).
(Replacing solvent molecule)
Placed Cl- in aa at (-2.08, 10.85, 35.55).
(Replacing solvent molecule)
Placed Na+ in aa at (-2.42, 17.76, 33.80).
(Replacing solvent molecule)
Placed Cl- in aa at (1.91, 17.58, 33.56).
(Replacing solvent molecule)
Placed Na+ in aa at (-0.27, 13.96, 37.63).
(Replacing solvent molecule)
Placed Cl- in aa at (-4.70, 12.61, 39.54).
(Replacing solvent molecule)
Placed Na+ in aa at (-1.59, 6.04, 34.68).
(Replacing solvent molecule)
Placed Cl- in aa at (2.47, 8.26, 32.92).
(Replacing solvent molecule)
Placed Na+ in aa at (5.04, 10.34, 30.35).
(Replacing solvent molecule)
Placed Cl- in aa at (-4.09, 6.52, 37.00).
(Replacing solvent molecule)
Placed Na+ in aa at (-7.53, 8.20, 39.16).
(Replacing solvent molecule)
Placed Cl- in aa at (27.97, 12.56, -25.48).
(Replacing solvent molecule)
Placed Na+ in aa at (24.93, 9.79, -25.61).
(Replacing solvent molecule)
Placed Cl- in aa at (22.43, 9.20, -28.53).
(Replacing solvent molecule)
Placed Na+ in aa at (19.86, 6.58, -28.66).
(Replacing solvent molecule)
Placed Cl- in aa at (-20.72, 14.74, 25.09).
(Replacing solvent molecule)
Placed Na+ in aa at (-21.84, 13.06, 27.13).
(Replacing solvent molecule)
Placed Cl- in aa at (-23.87, 16.28, 28.76).

Done adding ions.
> addions aa Na+ 10 Cl- 10
Adding 20 counter ions to "aa" using 1A grid
Total solute charge:   0.00  Max atom radius:   2.47
Grid extends from solute vdw + 1.32  to  7.79
Box:
   enclosing:  -39.58 -45.78 -40.23   39.52 40.89 47.33
   sized:			      88.42 82.22 87.77
   edge:        128.00
Resolution:      1.00 Angstrom.
Tree depth: 7
grid build: 2 sec
Volume =  4.96% of box, grid points 104103
Solvent present: replacing closest with ion
	 when steric overlaps occur
Calculating grid charges
charges: 152 sec
(Replacing solvent molecule)
Placed Na+ in aa at (32.16, 9.85, -7.25).
(Replacing solvent molecule)
Placed Cl- in aa at (36.89, 3.27, -6.11).
(Replacing solvent molecule)
Placed Na+ in aa at (34.06, 3.95, -6.60).
(Replacing solvent molecule)
Placed Cl- in aa at (32.30, 7.74, -3.67).
(Replacing solvent molecule)
Placed Na+ in aa at (30.75, 7.15, -1.47).
(Replacing solvent molecule)
Placed Cl- in aa at (29.16, 9.51, 1.86).
(Replacing solvent molecule)
Placed Na+ in aa at (29.11, 13.15, 5.88).
(Replacing solvent molecule)
Placed Cl- in aa at (30.10, 17.76, 7.25).
(Replacing solvent molecule)
Placed Na+ in aa at (23.75, 21.71, 0.82).
(Replacing solvent molecule)
Placed Cl- in aa at (25.03, 24.79, 0.56).
(Replacing solvent molecule)
Placed Na+ in aa at (26.44, 19.33, 5.28).
(Replacing solvent molecule)
Placed Cl- in aa at (24.86, 16.56, 3.06).
(No solvent overlap)
Placed Na+ in aa at (21.42, 16.22, 4.77).
(Replacing solvent molecule)
Placed Cl- in aa at (24.62, 15.62, 8.65).
(Replacing solvent molecule)
Placed Na+ in aa at (27.39, 15.14, 10.27).
(Replacing solvent molecule)
Placed Cl- in aa at (25.84, 16.36, 15.22).
(Replacing solvent molecule)
Placed Na+ in aa at (24.15, 15.92, 19.65).
(Replacing solvent molecule)
Placed Cl- in aa at (20.06, 16.75, 17.41).
(Replacing solvent molecule)
Placed Na+ in aa at (19.37, 25.66, 9.98).
(Replacing solvent molecule)
Placed Cl- in aa at (20.82, 27.85, 7.52).

Done adding ions.
> addions aa Na+ 10 Cl- 10
Adding 20 counter ions to "aa" using 1A grid
Total solute charge:   0.00  Max atom radius:   2.47
Grid extends from solute vdw + 1.32  to  7.79
Box:
   enclosing:  -39.58 -45.78 -40.23   44.68 40.89 47.33
   sized:			      88.42 82.22 87.77
   edge:        128.00
Resolution:      1.00 Angstrom.
Tree depth: 7
grid build: 2 sec
Volume =  5.09% of box, grid points 106740
Solvent present: replacing closest with ion
	 when steric overlaps occur
Calculating grid charges
charges: 155 sec
(Replacing solvent molecule)
Placed Na+ in aa at (27.00, 9.29, 14.74).
(Replacing solvent molecule)
Placed Cl- in aa at (27.82, 12.61, 12.99).
(Replacing solvent molecule)
Placed Na+ in aa at (29.93, 16.82, 13.75).
(Replacing solvent molecule)
Placed Cl- in aa at (32.25, 13.96, 11.08).
(Replacing solvent molecule)
Placed Na+ in aa at (30.98, 10.93, 13.67).
(Replacing solvent molecule)
Placed Cl- in aa at (30.55, 7.30, 13.61).
(Replacing solvent molecule)
Placed Na+ in aa at (19.91, 14.81, 11.81).
(Replacing solvent molecule)
Placed Cl- in aa at (15.13, 25.72, 11.54).
(Replacing solvent molecule)
Placed Na+ in aa at (16.86, 26.20, 8.94).
(Replacing solvent molecule)
Placed Cl- in aa at (6.10, -9.04, 9.28).
(Replacing solvent molecule)
Placed Na+ in aa at (8.24, -6.87, 12.75).
(Replacing solvent molecule)
Placed Cl- in aa at (8.65, -6.71, 15.48).
(Replacing solvent molecule)
Placed Na+ in aa at (6.49, -9.89, 19.41).
(Replacing solvent molecule)
Placed Cl- in aa at (5.04, -12.66, 17.08).
(Replacing solvent molecule)
Placed Na+ in aa at (4.16, -14.30, 15.22).
(Replacing solvent molecule)
Placed Cl- in aa at (3.27, -19.03, 12.60).
(Replacing solvent molecule)
Placed Na+ in aa at (2.14, -20.47, 10.41).
(Replacing solvent molecule)
Placed Cl- in aa at (3.23, -16.48, 21.63).
(Replacing solvent molecule)
Placed Na+ in aa at (0.52, -20.02, 21.73).
(Replacing solvent molecule)
Placed Cl- in aa at (14.98, -14.89, 9.76).

Done adding ions.
> 
> saveamberparm aa b13.topo b13.coords
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 ** Warning: No sp2 improper torsion term for  C*-CN-CB-CA
        atoms are: CG CE2 CD2 CE3
 ** Warning: No sp2 improper torsion term for  NA-CA-CN-CB
        atoms are: NE1 CZ2 CE2 CD2
 ** Warning: No sp2 improper torsion term for  C*-CN-CB-CA
        atoms are: CG CE2 CD2 CE3
 ** Warning: No sp2 improper torsion term for  NA-CA-CN-CB
        atoms are: NE1 CZ2 CE2 CD2
 ** Warning: No sp2 improper torsion term for  C*-CN-CB-CA
        atoms are: CG CE2 CD2 CE3
 ** Warning: No sp2 improper torsion term for  NA-CA-CN-CB
        atoms are: NE1 CZ2 CE2 CD2
 total 1520 improper torsions applied
Building H-Bond parameters.
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

	CTHR	1
	HEM	1
	NHIE	1
	OHT	1
	WAT	17084
  )
 (no restraints)
> 
 
> quit
	Quit