log started: Tue Oct 22 14:47:39 2013

Log file: ./leap.log
> #
> # ----- leaprc for loading the ff99SB (Hornak & Simmerling) force field
> # -----  this file is updated for PDB format 3
> #
> #	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" }
> 	{ "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"  "Ca" "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: /home/kyleb/src/amber12//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: 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: /home/kyleb/src/amber12//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: /home/kyleb/src/amber12//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: /home/kyleb/src/amber12//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: /home/kyleb/src/amber12//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: /home/kyleb/src/amber12//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: /home/kyleb/src/amber12//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: /home/kyleb/src/amber12//dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: MEOHBOX
Loading: NMABOX
Loading: PL3
Loading: POL3BOX
Loading: QSPCFWBOX
Loading: SPC
Loading: SPCBOX
Loading: SPCFWBOX
Loading: SPF
Loading: SPG
Loading: T4E
Loading: TIP3PBOX
Loading: TIP3PFBOX
Loading: TIP4PBOX
Loading: TIP4PEWBOX
Loading: TIP5PBOX
Loading: TP3
Loading: TP4
Loading: TP5
Loading: TPF
> HOH = TP3
> WAT = TP3
> 
> #
> #	Define the PDB name map for the amino acids and 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" "RG5"  } { 1 "G" "RG3"  } { "G" "RG" } { "GN" "RGN" }
>   { 0 "A" "RA5"  } { 1 "A" "RA3"  } { "A" "RA" } { "AN" "RAN" }
>   { 0 "C" "RC5"  } { 1 "C" "RC3"  } { "C" "RC" } { "CN" "RCN" }
>   { 0 "U" "RU5"  } { 1 "U" "RU3"  } { "U" "RU" } { "UN" "RUN" }
>   { 0 "DG" "DG5"  } { 1 "DG" "DG3"  }  
>   { 0 "DA" "DA5"  } { 1 "DA" "DA3"  }  
>   { 0 "DC" "DC5"  } { 1 "DC" "DC3"  }  
>   { 0 "DT" "DT5"  } { 1 "DT" "DT3"  }
> 
> }
> 
> addPdbAtomMap {
>   { "O5*" "O5'" }
>   { "C5*" "C5'" }
>   { "C4*" "C4'" }
>   { "O4*" "O4'" }
>   { "C3*" "C3'" }
>   { "O3*" "O3'" }
>   { "C2*" "C2'" }
>   { "C1*" "C1'" }
>   { "C5M" "C7"  }
>   { "O2*" "O2'" }
>   { "H1*" "H1'" }
>   { "H2*1" "H2'1" }
>   { "H2*2" "H2'2" }
>   { "H2'"  "H2'1" }
>   { "H2''" "H2'2" }
>   { "H3*" "H3'" }
>   { "H4*" "H4'" }
>   { "H5*1" "H5'1" }
>   { "H5*2" "H5'2" }
>   { "H5'"  "H5'1" }
>   { "H5''" "H5'2" }
>   { "HO2'" "HO'2" }
>   { "HO5'" "H5T" }
>   { "HO3'" "H3T" }
>   { "O1'" "O4'" }
>   { "OA"  "O1P" }
>   { "OB"  "O2P" }
>   { "OP1" "O1P" }
>   { "OP2" "O2P" }
> }
> 
> 
> #
> # assumed that most often proteins use HIE
> #
> NHIS = NHIE
> HIS = HIE
> CHIS = CHIE
 
> source leaprc.gaff
----- Source: /home/kyleb/src/amber12//dat/leap/cmd/leaprc.gaff
----- Source of /home/kyleb/src/amber12//dat/leap/cmd/leaprc.gaff done
>> logFile leap.log
log started: Tue Oct 22 14:47:42 2013

Log file: ./leap.log
>> #
>> # ----- leaprc for loading the general Amber Force field.
>> #       This file is mostly for use with Antechamber
>> #
>> #	load atom type hybridizations
>> #
>> addAtomTypes {
>> 	{ "h1"  "H" "sp3" }
>> 	{ "h2"  "H" "sp3" }
>> 	{ "h3"  "H" "sp3" }
>> 	{ "h4"  "H" "sp3" }
>> 	{ "h5"  "H" "sp3" }
>> 	{ "ha"  "H" "sp3" }
>> 	{ "hc"  "H" "sp3" }
>> 	{ "hn"  "H" "sp3" }
>> 	{ "ho"  "H" "sp3" }
>> 	{ "hp"  "H" "sp3" }
>> 	{ "hs"  "H" "sp3" }
>> 	{ "hw"  "H" "sp3" }
>> 	{ "hx"  "H" "sp3" }
>> 	{ "o"  "O" "sp2" }
>> 	{ "o2"  "O" "sp2" }
>> 	{ "oh"  "O" "sp3" }
>> 	{ "os"  "O" "sp3" }
>> 	{ "ow"  "O" "sp3" }
>> 	{ "c"  "C" "sp2" }
>> 	{ "c1"  "C" "sp2" }
>> 	{ "c2"  "C" "sp2" }
>> 	{ "c3"  "C" "sp3" }
>> 	{ "ca"  "C" "sp2" }
>> 	{ "cc"  "C" "sp2" }
>> 	{ "cd"  "C" "sp2" }
>> 	{ "ce"  "C" "sp2" }
>> 	{ "cf"  "C" "sp2" }
>> 	{ "cg"  "C" "sp2" }
>> 	{ "ch"  "C" "sp2" }
>> 	{ "cp"  "C" "sp2" }
>> 	{ "cq"  "C" "sp2" }
>> 	{ "cu"  "C" "sp2" }
>> 	{ "cv"  "C" "sp2" }
>> 	{ "cx"  "C" "sp2" }
>> 	{ "cy"  "C" "sp2" }
>> 	{ "n"   "N" "sp2" }
>> 	{ "n1"  "N" "sp2" }
>> 	{ "n2"  "N" "sp2" }
>> 	{ "n3"  "N" "sp3" }
>> 	{ "n4"  "N" "sp3" }
>> 	{ "na"  "N" "sp2" }
>> 	{ "nb"  "N" "sp2" }
>> 	{ "nc"  "N" "sp2" }
>> 	{ "nd"  "N" "sp2" }
>> 	{ "ne"  "N" "sp2" }
>> 	{ "nf"  "N" "sp2" }
>> 	{ "nh"  "N" "sp2" }
>> 	{ "no"  "N" "sp2" }
>> 	{ "s"   "S" "sp2" }
>> 	{ "s2"   "S" "sp2" }
>> 	{ "s3"   "S" "sp3" }
>> 	{ "s4"   "S" "sp3" }
>> 	{ "s6"   "S" "sp3" }
>> 	{ "sh"   "S" "sp3" }
>> 	{ "ss"   "S" "sp3" }
>> 	{ "sx"   "S" "sp3" }
>> 	{ "sy"   "S" "sp3" }
>> 	{ "p2"   "P" "sp2" }
>> 	{ "p3"   "P" "sp3" }
>> 	{ "p4"   "P" "sp3" }
>> 	{ "p5"   "P" "sp3" }
>> 	{ "pb"   "P" "sp3" }
>> 	{ "pd"   "P" "sp3" }
>> 	{ "px"   "P" "sp3" }
>> 	{ "py"   "P" "sp3" }
>> 	{ "f"   "F" "sp3" }
>> 	{ "cl"  "Cl" "sp3" }
>> 	{ "br"  "Br" "sp3" }
>> 	{ "i"   "I"  "sp3" }
>> }
>> #
>> #	Load the general force field parameter set.
>> #
>> gaff = loadamberparams gaff.dat
Loading parameters: /home/kyleb/src/amber12//dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.4, March 2010) add. info. at the end
(UNKNOWN ATOM TYPE: cz)
> 
> SUS = loadmol2 benzene.mol2
Loading Mol2 file: ./benzene.mol2
Reading MOLECULE named LIG
> check SUS
Checking 'SUS'....
Checking parameters for unit 'SUS'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
> loadamberparams benzene.frcmod
Loading parameters: ./benzene.frcmod
Reading force field modification type file (frcmod)
Reading title:
remark goes here
> saveoff SUS benzene.lib
 Creating benzene.lib
Saving SUS.
Building topology.
Building atom parameters.
> saveamberparm SUS benzene.prmtop benzene.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 6 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

	LIG	1
  )
 (no restraints)
> quit
	Quit
log started: Tue Oct 22 19:21:20 2013

Log file: ./leap.log
>> #
>> # ----- leaprc for loading the ff99SB (Hornak & Simmerling) force field
>> # -----  this file is updated for PDB format 3
>> #
>> #	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" }
>> 	{ "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"  "Ca" "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: /home/kyleb/src/amber12//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: 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: /home/kyleb/src/amber12//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: /home/kyleb/src/amber12//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: /home/kyleb/src/amber12//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: /home/kyleb/src/amber12//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: /home/kyleb/src/amber12//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: /home/kyleb/src/amber12//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: /home/kyleb/src/amber12//dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: MEOHBOX
Loading: NMABOX
Loading: PL3
Loading: POL3BOX
Loading: QSPCFWBOX
Loading: SPC
Loading: SPCBOX
Loading: SPCFWBOX
Loading: SPF
Loading: SPG
Loading: T4E
Loading: TIP3PBOX
Loading: TIP3PFBOX
Loading: TIP4PBOX
Loading: TIP4PEWBOX
Loading: TIP5PBOX
Loading: TP3
Loading: TP4
Loading: TP5
Loading: TPF
>> HOH = TP3
>> WAT = TP3
>> 
>> #
>> #	Define the PDB name map for the amino acids and 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" "RG5"  } { 1 "G" "RG3"  } { "G" "RG" } { "GN" "RGN" }
>>   { 0 "A" "RA5"  } { 1 "A" "RA3"  } { "A" "RA" } { "AN" "RAN" }
>>   { 0 "C" "RC5"  } { 1 "C" "RC3"  } { "C" "RC" } { "CN" "RCN" }
>>   { 0 "U" "RU5"  } { 1 "U" "RU3"  } { "U" "RU" } { "UN" "RUN" }
>>   { 0 "DG" "DG5"  } { 1 "DG" "DG3"  }  
>>   { 0 "DA" "DA5"  } { 1 "DA" "DA3"  }  
>>   { 0 "DC" "DC5"  } { 1 "DC" "DC3"  }  
>>   { 0 "DT" "DT5"  } { 1 "DT" "DT3"  }
>> 
>> }
>> 
>> addPdbAtomMap {
>>   { "O5*" "O5'" }
>>   { "C5*" "C5'" }
>>   { "C4*" "C4'" }
>>   { "O4*" "O4'" }
>>   { "C3*" "C3'" }
>>   { "O3*" "O3'" }
>>   { "C2*" "C2'" }
>>   { "C1*" "C1'" }
>>   { "C5M" "C7"  }
>>   { "O2*" "O2'" }
>>   { "H1*" "H1'" }
>>   { "H2*1" "H2'1" }
>>   { "H2*2" "H2'2" }
>>   { "H2'"  "H2'1" }
>>   { "H2''" "H2'2" }
>>   { "H3*" "H3'" }
>>   { "H4*" "H4'" }
>>   { "H5*1" "H5'1" }
>>   { "H5*2" "H5'2" }
>>   { "H5'"  "H5'1" }
>>   { "H5''" "H5'2" }
>>   { "HO2'" "HO'2" }
>>   { "HO5'" "H5T" }
>>   { "HO3'" "H3T" }
>>   { "O1'" "O4'" }
>>   { "OA"  "O1P" }
>>   { "OB"  "O2P" }
>>   { "OP1" "O1P" }
>>   { "OP2" "O2P" }
>> }
>> 
>> 
>> #
>> # assumed that most often proteins use HIE
>> #
>> NHIS = NHIE
>> HIS = HIE
>> CHIS = CHIE
> 
> source leaprc.gaff
----- Source: /home/kyleb/src/amber12//dat/leap/cmd/leaprc.gaff
----- Source of /home/kyleb/src/amber12//dat/leap/cmd/leaprc.gaff done
>> logFile leap.log
log started: Tue Oct 22 19:21:21 2013

Log file: ./leap.log
>> #
>> # ----- leaprc for loading the general Amber Force field.
>> #       This file is mostly for use with Antechamber
>> #
>> #	load atom type hybridizations
>> #
>> addAtomTypes {
>> 	{ "h1"  "H" "sp3" }
>> 	{ "h2"  "H" "sp3" }
>> 	{ "h3"  "H" "sp3" }
>> 	{ "h4"  "H" "sp3" }
>> 	{ "h5"  "H" "sp3" }
>> 	{ "ha"  "H" "sp3" }
>> 	{ "hc"  "H" "sp3" }
>> 	{ "hn"  "H" "sp3" }
>> 	{ "ho"  "H" "sp3" }
>> 	{ "hp"  "H" "sp3" }
>> 	{ "hs"  "H" "sp3" }
>> 	{ "hw"  "H" "sp3" }
>> 	{ "hx"  "H" "sp3" }
>> 	{ "o"  "O" "sp2" }
>> 	{ "o2"  "O" "sp2" }
>> 	{ "oh"  "O" "sp3" }
>> 	{ "os"  "O" "sp3" }
>> 	{ "ow"  "O" "sp3" }
>> 	{ "c"  "C" "sp2" }
>> 	{ "c1"  "C" "sp2" }
>> 	{ "c2"  "C" "sp2" }
>> 	{ "c3"  "C" "sp3" }
>> 	{ "ca"  "C" "sp2" }
>> 	{ "cc"  "C" "sp2" }
>> 	{ "cd"  "C" "sp2" }
>> 	{ "ce"  "C" "sp2" }
>> 	{ "cf"  "C" "sp2" }
>> 	{ "cg"  "C" "sp2" }
>> 	{ "ch"  "C" "sp2" }
>> 	{ "cp"  "C" "sp2" }
>> 	{ "cq"  "C" "sp2" }
>> 	{ "cu"  "C" "sp2" }
>> 	{ "cv"  "C" "sp2" }
>> 	{ "cx"  "C" "sp2" }
>> 	{ "cy"  "C" "sp2" }
>> 	{ "n"   "N" "sp2" }
>> 	{ "n1"  "N" "sp2" }
>> 	{ "n2"  "N" "sp2" }
>> 	{ "n3"  "N" "sp3" }
>> 	{ "n4"  "N" "sp3" }
>> 	{ "na"  "N" "sp2" }
>> 	{ "nb"  "N" "sp2" }
>> 	{ "nc"  "N" "sp2" }
>> 	{ "nd"  "N" "sp2" }
>> 	{ "ne"  "N" "sp2" }
>> 	{ "nf"  "N" "sp2" }
>> 	{ "nh"  "N" "sp2" }
>> 	{ "no"  "N" "sp2" }
>> 	{ "s"   "S" "sp2" }
>> 	{ "s2"   "S" "sp2" }
>> 	{ "s3"   "S" "sp3" }
>> 	{ "s4"   "S" "sp3" }
>> 	{ "s6"   "S" "sp3" }
>> 	{ "sh"   "S" "sp3" }
>> 	{ "ss"   "S" "sp3" }
>> 	{ "sx"   "S" "sp3" }
>> 	{ "sy"   "S" "sp3" }
>> 	{ "p2"   "P" "sp2" }
>> 	{ "p3"   "P" "sp3" }
>> 	{ "p4"   "P" "sp3" }
>> 	{ "p5"   "P" "sp3" }
>> 	{ "pb"   "P" "sp3" }
>> 	{ "pd"   "P" "sp3" }
>> 	{ "px"   "P" "sp3" }
>> 	{ "py"   "P" "sp3" }
>> 	{ "f"   "F" "sp3" }
>> 	{ "cl"  "Cl" "sp3" }
>> 	{ "br"  "Br" "sp3" }
>> 	{ "i"   "I"  "sp3" }
>> }
>> #
>> #	Load the general force field parameter set.
>> #
>> gaff = loadamberparams gaff.dat
Loading parameters: /home/kyleb/src/amber12//dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.4, March 2010) add. info. at the end
(UNKNOWN ATOM TYPE: cz)
> 
> LIG = loadmol2 benzene.mol2 
Loading Mol2 file: ./benzene.mol2
Reading MOLECULE named LIG
> check LIG
Checking 'LIG'....
Checking parameters for unit 'LIG'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
> loadamberparams benzene.frcmod
Loading parameters: ./benzene.frcmod
Reading force field modification type file (frcmod)
Reading title:
remark goes here
> saveoff LIG benzene.lib
Saving LIG.
Building topology.
Building atom parameters.
> saveamberparm LIG benzene.prmtop benzene.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 6 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

	LIG	1
  )
 (no restraints)
> quit
	Quit
