log started: Tue Oct 22 15:58:48 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 15:58:50 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 propene.mol2
Loading Mol2 file: ./propene.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 propene.frcmod
Loading parameters: ./propene.frcmod
Reading force field modification type file (frcmod)
Reading title:
remark goes here
> saveoff SUS propene.lib
 Creating propene.lib
Saving SUS.
Building topology.
Building atom parameters.
> saveamberparm SUS propene.prmtop propene.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 2 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 17:53:34 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 17:53:39 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 propene.mol2
Loading Mol2 file: ./propene.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 propene.frcmod
Loading parameters: ./propene.frcmod
Reading force field modification type file (frcmod)
Reading title:
remark goes here
> list
ACE       ALA       ARG       ASH       ASN       ASP       CALA      CARG      
CASN      CASP      CCYS      CCYX      CGLN      CGLU      CGLY      CHCL3BOX  
CHID      CHIE      CHIP      CHIS      CILE      CIO       CLEU      CLYS      
CMET      CPHE      CPRO      CSER      CTHR      CTRP      CTYR      CVAL      
CYM       CYS       CYX       Cl-       Cs+       DA        DA3       DA5       
DAN       DC        DC3       DC4       DC5       DCN       DG        DG3       
DG5       DGN       DT        DT3       DT5       DTN       GLH       GLN       
GLU       GLY       HID       HIE       HIP       HIS       HOH       IB        
ILE       K+        LEU       LYN       LYS       Li+       MEOHBOX   MET       
MG2       NALA      NARG      NASN      NASP      NCYS      NCYX      NGLN      
NGLU      NGLY      NHE       NHID      NHIE      NHIP      NHIS      NILE      
NLEU      NLYS      NMABOX    NME       NMET      NPHE      NPRO      NSER      
NTHR      NTRP      NTYR      NVAL      Na+       PHE       PL3       POL3BOX   
PRO       QSPCFWBOX RA        RA3       RA5       RAN       RC        RC3       
RC5       RCN       RG        RG3       RG5       RGN       RU        RU3       
RU5       RUN       Rb+       SER       SPC       SPCBOX    SPCFWBOX  SPF       
SPG       SUS       T4E       THR       TIP3PBOX  TIP3PFBOX TIP4PBOX  TIP4PEWBOX
TIP5PBOX  TP3       TP4       TP5       TPF       TRP       TYR       VAL       
WAT       frcmod99SBgaff      parm99    
> help SUS
help: Argument #1 is type Unit must be of type: [string]
usage:  help <command>
> help
Help is available on the following subjects:

_cmd_options_       _types_             add                 addAtomTypes
addH                addIons             addIons2            addIonsRand
addPath             addPdbAtomMap       addPdbResMap        alias
alignAxes           bond                bondByDistance      center
charge              check               clearPdbAtomMap     clearPdbResMap
clearVariables      combine             copy                createAtom
createParmset       createResidue       createUnit          crossLink
debugOff            debugOn             debugStatus         deleteBond
deleteOffLibEntry   deleteRestraint     desc                deSelect
displayPdbAtomMap   displayPdbResMap    edit                flip
groupSelectedAtoms  help                impose              list
listOff             loadAmberParams     loadAmberPrep       loadMol2
loadMol3            loadOff             loadPdb             loadPdbUsingSeq
logFile             matchVariables      measureGeom         quit
relax               remove              restrainAngle       restrainBond
restrainTorsion     saveAmberParm       saveAmberParmPert   saveAmberParmPol
saveAmberParmPolPertsaveAmberPrep       saveMol2            saveMol3
saveOff             saveOffParm         savePdb             scaleCharges
select              sequence            set                 setBox
showdefault         solvateBox          solvateCap          solvateDontClip
solvateOct          solvateShell        source              transform
translate           verbosity           zMatrix             

For a list of the current aliases, type "alias".
> list
ACE       ALA       ARG       ASH       ASN       ASP       CALA      CARG      
CASN      CASP      CCYS      CCYX      CGLN      CGLU      CGLY      CHCL3BOX  
CHID      CHIE      CHIP      CHIS      CILE      CIO       CLEU      CLYS      
CMET      CPHE      CPRO      CSER      CTHR      CTRP      CTYR      CVAL      
CYM       CYS       CYX       Cl-       Cs+       DA        DA3       DA5       
DAN       DC        DC3       DC4       DC5       DCN       DG        DG3       
DG5       DGN       DT        DT3       DT5       DTN       GLH       GLN       
GLU       GLY       HID       HIE       HIP       HIS       HOH       IB        
ILE       K+        LEU       LYN       LYS       Li+       MEOHBOX   MET       
MG2       NALA      NARG      NASN      NASP      NCYS      NCYX      NGLN      
NGLU      NGLY      NHE       NHID      NHIE      NHIP      NHIS      NILE      
NLEU      NLYS      NMABOX    NME       NMET      NPHE      NPRO      NSER      
NTHR      NTRP      NTYR      NVAL      Na+       PHE       PL3       POL3BOX   
PRO       QSPCFWBOX RA        RA3       RA5       RAN       RC        RC3       
RC5       RCN       RG        RG3       RG5       RGN       RU        RU3       
RU5       RUN       Rb+       SER       SPC       SPCBOX    SPCFWBOX  SPF       
SPG       SUS       T4E       THR       TIP3PBOX  TIP3PFBOX TIP4PBOX  TIP4PEWBOX
TIP5PBOX  TP3       TP4       TP5       TPF       TRP       TYR       VAL       
WAT       frcmod99SBgaff      parm99    
> list SUS
list: Improper number of arguments!
usage:  list
> verbosity
verbosity: Improper number of arguments!
usage:  verbosity <level>
> verbosity 1
Verbosity level: 1
> debugOn
debugOn: Improper number of arguments!
usage:  debugOn <filename>
> select SUS
> desc
desc: Improper number of arguments!
usage:  desc <variable>
> desc SUS
UNIT name: LIG
Head atom: null
Tail atom: null
Contents: 
R<LIG 1>
> desc LIG
STRING (with no reference): 'LIG'
> quit
	Quit
log started: Tue Oct 22 19:22:47 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 19:22:47 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 propene.mol2 
Loading Mol2 file: ./propene.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 propene.frcmod
Loading parameters: ./propene.frcmod
Reading force field modification type file (frcmod)
Reading title:
remark goes here
> saveoff LIG propene.lib
Saving LIG.
Building topology.
Building atom parameters.
> saveamberparm LIG propene.prmtop propene.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 2 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
