log started: Mon Jul 29 11:02:56 2019

Log file: ./leap.log
>> #
>> # ----- leaprc for loading the ff14SB force field
>> # ----- NOTE: this is designed 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" }
>> 	{ "HZ"  "H" "sp3" }
>> 	{ "OH"  "O" "sp3" }
>> 	{ "OS"  "O" "sp3" }
>> 	{ "O"   "O" "sp2" }
>> 	{ "O2"  "O" "sp2" }
>> 	{ "OP"  "O" "sp2" }
>> 	{ "OW"  "O" "sp3" }
>> 	{ "CT"  "C" "sp3" }
>> 	{ "CX"  "C" "sp3" }
>> 	{ "C8"  "C" "sp3" }
>> 	{ "2C"  "C" "sp3" }
>> 	{ "3C"  "C" "sp3" }
>> 	{ "CH"  "C" "sp3" }
>> 	{ "CS"  "C" "sp2" }
>> 	{ "C"   "C" "sp2" }
>> 	{ "CO"   "C" "sp2" }
>> 	{ "C*"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CB"  "C" "sp2" }
>> 	{ "CC"  "C" "sp2" }
>> 	{ "CN"  "C" "sp2" }
>> 	{ "CM"  "C" "sp2" }
>> 	{ "CK"  "C" "sp2" }
>> 	{ "CQ"  "C" "sp2" }
>> 	{ "CD"  "C" "sp2" }
>> 	{ "C5"  "C" "sp2" }
>> 	{ "C4"  "C" "sp2" }
>> 	{ "CP"  "C" "sp2" }
>> 	{ "CI"  "C" "sp3" }
>> 	{ "CJ"  "C" "sp2" }
>> 	{ "CW"  "C" "sp2" }
>> 	{ "CV"  "C" "sp2" }
>> 	{ "CR"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CY"  "C" "sp2" }
>> 	{ "C0"  "Ca" "sp3" }
>> 	{ "MG"  "Mg" "sp3" }
>> 	{ "N"   "N" "sp2" }
>> 	{ "NA"  "N" "sp2" }
>> 	{ "N2"  "N" "sp2" }
>> 	{ "N*"  "N" "sp2" }
>> 	{ "NP"  "N" "sp2" }
>> 	{ "NQ"  "N" "sp2" }
>> 	{ "NB"  "N" "sp2" }
>> 	{ "NC"  "N" "sp2" }
>> 	{ "NT"  "N" "sp3" }
>> 	{ "NY"  "N" "sp2" }
>> 	{ "N3"  "N" "sp3" }
>> 	{ "S"   "S" "sp3" }
>> 	{ "SH"  "S" "sp3" }
>> 	{ "P"   "P" "sp3" }
>> 	{ "LP"  ""  "sp3" }
>> 	{ "EP"  ""  "sp3" }
>> 	{ "F"   "F" "sp3" }
>> 	{ "Cl"  "Cl" "sp3" }
>> 	{ "Br"  "Br" "sp3" }
>> 	{ "I"   "I"  "sp3" }
>> }
>> #
>> #	Load the main parameter set.
>> #
>> parm10 = loadamberparams parm10.dat
Loading parameters: /home/ravi/anaconda3/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
>> frcmod14SB = loadamberparams frcmod.ff14SB
Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.ff14SB
Reading force field modification type file (frcmod)
Reading title:
ff14SB protein backbone and sidechain parameters
>> #
>> #	Load main chain and terminating amino acid libraries
>> #
>> loadOff amino12.lib
Loading library: /home/ravi/anaconda3/dat/leap/lib/amino12.lib
Loading: ALA
Loading: ARG
Loading: ASH
Loading: ASN
Loading: ASP
Loading: CYM
Loading: CYS
Loading: CYX
Loading: GLH
Loading: GLN
Loading: GLU
Loading: GLY
Loading: HID
Loading: HIE
Loading: HIP
Loading: HYP
Loading: ILE
Loading: LEU
Loading: LYN
Loading: LYS
Loading: MET
Loading: PHE
Loading: PRO
Loading: SER
Loading: THR
Loading: TRP
Loading: TYR
Loading: VAL
>> loadOff aminoct12.lib
Loading library: /home/ravi/anaconda3/dat/leap/lib/aminoct12.lib
Loading: CALA
Loading: CARG
Loading: CASN
Loading: CASP
Loading: CCYS
Loading: CCYX
Loading: CGLN
Loading: CGLU
Loading: CGLY
Loading: CHID
Loading: CHIE
Loading: CHIP
Loading: CHYP
Loading: CILE
Loading: CLEU
Loading: CLYS
Loading: CMET
Loading: CPHE
Loading: CPRO
Loading: CSER
Loading: CTHR
Loading: CTRP
Loading: CTYR
Loading: CVAL
Loading: NHE
Loading: NME
>> loadOff aminont12.lib
Loading library: /home/ravi/anaconda3/dat/leap/lib/aminont12.lib
Loading: ACE
Loading: NALA
Loading: NARG
Loading: NASN
Loading: NASP
Loading: NCYS
Loading: NCYX
Loading: NGLN
Loading: NGLU
Loading: NGLY
Loading: NHID
Loading: NHIE
Loading: NHIP
Loading: NILE
Loading: NLEU
Loading: NLYS
Loading: NMET
Loading: NPHE
Loading: NPRO
Loading: NSER
Loading: NTHR
Loading: NTRP
Loading: NTYR
Loading: NVAL
>> 
>> #
>> #	Define the PDB name map for the amino acids
>> #
>> addPdbResMap {
>>   { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" }
>>   { 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
>>   { 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
>>   { 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
>>   { 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
>>   { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
>>   { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
>>   { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
>>   { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
>>   { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
>>   { 0 "HID" "NHID" } { 1 "HID" "CHID" }
>>   { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
>>   { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
>>   { 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
>>   { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
>>   { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
>>   { 0 "MET" "NMET" } { 1 "MET" "CMET" }
>>   { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
>>   { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
>>   { 0 "SER" "NSER" } { 1 "SER" "CSER" }
>>   { 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
>>   { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
>>   { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
>>   { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
>>   { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
>> }
>> 
>> #
>> # assume that most often proteins use HIE
>> #
>> NHIS = NHIE
>> HIS = HIE
>> CHIS = CHIE
> 
> source leaprc.water.tip3p
----- Source: /home/ravi/anaconda3/dat/leap/cmd/leaprc.water.tip3p
----- Source of /home/ravi/anaconda3/dat/leap/cmd/leaprc.water.tip3p done
>> #
>> #       Load water and ions for TIP3P + Li/Merz monovalent ions 
>> #       + Joung-Chetham monovalent ions
>> #       + Li/Merz highly charged ions (+2 to +4, 12-6 normal usage set)
>> #
>> #       Note: the Li/Merz monovalent set is loaded only to get Tl+,
>> #          Cu+, Ag+ NH4+, H3O+.  Since we load Joung-Cheatham second,
>> #          the alkali halide parameters come from the Joung-Cheatham set
>> #
>> addAtomTypes {
>> 	{ "HW"  "H" "sp3" }
>> 	{ "OW"  "O" "sp3" }
>> 	{ "F-"   "F" "sp3" }
>> 	{ "Cl-"  "Cl" "sp3" }
>> 	{ "Br-"  "Br" "sp3" }
>> 	{ "I-"   "I"  "sp3" }
>> 	{ "Li+"  "Li"  "sp3" }
>> 	{ "Na+"  "Na"  "sp3" }
>> 	{ "K+"  "K"  "sp3" }
>> 	{ "Rb+"  "Rb"  "sp3" }
>> 	{ "Cs+"  "Cs"  "sp3" }
>> 	{ "Mg+"  "Mg"  "sp3" }
>>     { "Tl+"  "Tl"  "sp3" }
>>     { "Cu+"  "Cu"  "sp3" }
>>     { "Ag+"  "Ag"  "sp3" }
>>     { "NH4+"  "N"  "sp3" }
>>     { "H3O+"  "O"  "sp3" }
>>     { "Be2+" "Be"  "sp3" }
>>     { "Cu2+" "Cu"  "sp3" }
>>     { "Ni2+" "Ni"  "sp3" }
>>     { "Pt2+" "Pt"  "sp3" }
>>     { "Zn2+" "Zn"  "sp3" }
>>     { "Co2+" "Co"  "sp3" }
>>     { "Pd2+" "Pd"  "sp3" }
>>     { "Ag2+" "Ag"  "sp3" }
>>     { "Cr2+" "Cr"  "sp3" }
>>     { "Fe2+" "Fe"  "sp3" }
>>     { "Mg2+" "Mg"  "sp3" }
>>     { "V2+"  "V"   "sp3" }
>>     { "Mn2+" "Mn"  "sp3" }
>>     { "Hg2+" "Hg"  "sp3" }
>>     { "Cd2+" "Cd"  "sp3" }
>>     { "Yb2+" "Yb"  "sp3" }
>>     { "Ca2+" "Ca"  "sp3" }
>>     { "Sn2+" "Sn"  "sp3" }
>>     { "Pb2+" "Pb"  "sp3" }
>>     { "Eu2+" "Eu"  "sp3" }
>>     { "Sr2+" "Sr"  "sp3" }
>>     { "Sm2+" "Sm"  "sp3" }
>>     { "Ba2+" "Ba"  "sp3" }
>>     { "Ra2+" "Ra"  "sp3" }
>>     { "Al3+" "Al"  "sp3" }
>>     { "Fe3+" "Fe"  "sp3" }
>>     { "Cr3+" "Cr"  "sp3" }
>>     { "In3+" "In"  "sp3" }
>>     { "Tl3+" "Tl"  "sp3" }
>>     { "Y3+"  "Y"   "sp3" }
>>     { "La3+" "La"  "sp3" }
>>     { "Ce3+" "Ce"  "sp3" }
>>     { "Pr3+" "Pr"  "sp3" }
>>     { "Nd3+" "Nd"  "sp3" }
>>     { "Sm3+" "Sm"  "sp3" }
>>     { "Eu3+" "Eu"  "sp3" }
>>     { "Gd3+" "Gd"  "sp3" }
>>     { "Tb3+" "Tb"  "sp3" }
>>     { "Dy3+" "Dy"  "sp3" }
>>     { "Er3+" "Er"  "sp3" }
>>     { "Tm3+" "Tm"  "sp3" }
>>     { "Lu3+" "Lu"  "sp3" }
>>     { "Hf4+" "Hf"  "sp3" }
>>     { "Zr4+" "Zr"  "sp3" }
>>     { "Ce4+" "Ce"  "sp3" }
>>     { "U4+"  "U"   "sp3" }
>>     { "Pu4+" "Pu"  "sp3" }
>>     { "Th4+" "Th"  "sp3" }
>> }
>> loadOff atomic_ions.lib
Loading library: ./atomic_ions.lib
Loading: ZN
>> loadOff solvents.lib
Loading library: /home/ravi/anaconda3/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: FB3
Loading: FB3BOX
Loading: FB4
Loading: FB4BOX
Loading: MEOHBOX
Loading: NMABOX
Loading: OP3
Loading: OPC
Loading: OPC3BOX
Loading: OPCBOX
Loading: PL3
Loading: POL3BOX
Loading: QSPCFWBOX
Loading: SPC
Loading: SPCBOX
Loading: SPCFWBOX
Loading: SPF
Loading: SPG
Loading: T4E
Loading: TIP3PBOX
Loading: TIP3PFBOX
Loading: TIP4PBOX
Loading: TIP4PEWBOX
Loading: TIP5PBOX
Loading: TP3
Loading: TP4
Loading: TP5
Loading: TPF
>> HOH = TP3
>> WAT = TP3
>> loadAmberParams frcmod.tip3p
Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.tip3p
Reading force field modification type file (frcmod)
Reading title:
This is the additional/replacement parameter set for TIP3P water
>> loadAmberParams frcmod.ions1lm_126_tip3p
Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.ions1lm_126_tip3p
Reading force field modification type file (frcmod)
Reading title:
Li/Merz ion parameters of monovalent ions for TIP3P water model (12-6 normal usage set)
>> loadAmberParams frcmod.ionsjc_tip3p
Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.ionsjc_tip3p
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008)
>> loadAmberParams frcmod.ions234lm_126_tip3p
Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.ions234lm_126_tip3p
Reading force field modification type file (frcmod)
Reading title:
Li/Merz ion parameters of divalent to tetravalent ions for TIP3P water model (12-6 normal usage set)
>> 
> 
> source leaprc.gaff
----- Source: /home/ravi/anaconda3/dat/leap/cmd/leaprc.gaff
----- Source of /home/ravi/anaconda3/dat/leap/cmd/leaprc.gaff done
>> logFile leap.log
log started: Mon Jul 29 11:02:57 2019

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" }
>> 	{ "op"  "O" "sp3" }
>> 	{ "oq"  "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" }
>> 	{ "cz"  "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" }
>> 	{ "ni"  "N" "sp2" }
>> 	{ "nj"  "N" "sp2" }
>> 	{ "nk"  "N" "sp3" }
>> 	{ "nl"  "N" "sp3" }
>> 	{ "nm"  "N" "sp2" }
>> 	{ "nn"  "N" "sp2" }
>> 	{ "no"  "N" "sp2" }
>> 	{ "np"  "N" "sp3" }
>> 	{ "nq"  "N" "sp3" }
>> 	{ "s"   "S" "sp2" }
>> 	{ "s2"   "S" "sp2" }
>> 	{ "s3"   "S" "sp3" }
>> 	{ "s4"   "S" "sp3" }
>> 	{ "s6"   "S" "sp3" }
>> 	{ "sh"   "S" "sp3" }
>> 	{ "sp"   "S" "sp3" }
>> 	{ "sq"   "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" }
>> 	{ "pc"   "P" "sp3" }
>> 	{ "pd"   "P" "sp3" }
>> 	{ "pe"   "P" "sp3" }
>> 	{ "pf"   "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/ravi/anaconda3/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
> 
> list
ACE       ALA       ARG       ASH       ASN       ASP       CALA      CARG      
CASN      CASP      CCYS      CCYX      CGLN      CGLU      CGLY      CHCL3BOX  
CHID      CHIE      CHIP      CHIS      CHYP      CILE      CLEU      CLYS      
CMET      CPHE      CPRO      CSER      CTHR      CTRP      CTYR      CVAL      
CYM       CYS       CYX       DC4       FB3       FB3BOX    FB4       FB4BOX    
GLH       GLN       GLU       GLY       HID       HIE       HIP       HIS       
HOH       HYP       ILE       LEU       LYN       LYS       MEOHBOX   MET       
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      OP3       OPC       OPC3BOX   OPCBOX    PHE       
PL3       POL3BOX   PRO       QSPCFWBOX SER       SPC       SPCBOX    SPCFWBOX  
SPF       SPG       T4E       THR       TIP3PBOX  TIP3PFBOX TIP4PBOX  TIP4PEWBOX
TIP5PBOX  TP3       TP4       TP5       TPF       TRP       TYR       VAL       
WAT       ZN        frcmod14SBgaff      parm10