log started: Thu Oct 20 12:11:40 2022

Log file: ./leap.log
>> #
>> # ----- leaprc for loading the ff14SB force field
>> # ----- NOTE: this is designed for PDB format 3!
>> #    Uses frcmod.ff14SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA
>> #
>> #	load atom type hybridizations
>> #
>> addAtomTypes {
>> 	{ "H"   "H" "sp3" }
>> 	{ "HO"  "H" "sp3" }
>> 	{ "HS"  "H" "sp3" }
>> 	{ "H1"  "H" "sp3" }
>> 	{ "H2"  "H" "sp3" }
>> 	{ "H3"  "H" "sp3" }
>> 	{ "H4"  "H" "sp3" }
>> 	{ "H5"  "H" "sp3" }
>> 	{ "HW"  "H" "sp3" }
>> 	{ "HC"  "H" "sp3" }
>> 	{ "HA"  "H" "sp3" }
>> 	{ "HP"  "H" "sp3" }
>> 	{ "HZ"  "H" "sp3" }
>> 	{ "OH"  "O" "sp3" }
>> 	{ "OS"  "O" "sp3" }
>> 	{ "O"   "O" "sp2" }
>> 	{ "O2"  "O" "sp2" }
>> 	{ "OP"  "O" "sp2" }
>> 	{ "OW"  "O" "sp3" }
>> 	{ "CT"  "C" "sp3" }
>> 	{ "CX"  "C" "sp3" }
>> 	{ "C8"  "C" "sp3" }
>> 	{ "2C"  "C" "sp3" }
>> 	{ "3C"  "C" "sp3" }
>> 	{ "CH"  "C" "sp3" }
>> 	{ "CS"  "C" "sp2" }
>> 	{ "C"   "C" "sp2" }
>> 	{ "CO"   "C" "sp2" }
>> 	{ "C*"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CB"  "C" "sp2" }
>> 	{ "CC"  "C" "sp2" }
>> 	{ "CN"  "C" "sp2" }
>> 	{ "CM"  "C" "sp2" }
>> 	{ "CK"  "C" "sp2" }
>> 	{ "CQ"  "C" "sp2" }
>> 	{ "CD"  "C" "sp2" }
>> 	{ "C5"  "C" "sp2" }
>> 	{ "C4"  "C" "sp2" }
>> 	{ "CP"  "C" "sp2" }
>> 	{ "CI"  "C" "sp3" }
>> 	{ "CJ"  "C" "sp2" }
>> 	{ "CW"  "C" "sp2" }
>> 	{ "CV"  "C" "sp2" }
>> 	{ "CR"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CY"  "C" "sp2" }
>> 	{ "C0"  "Ca" "sp3" }
>> 	{ "MG"  "Mg" "sp3" }
>> 	{ "N"   "N" "sp2" }
>> 	{ "NA"  "N" "sp2" }
>> 	{ "N2"  "N" "sp2" }
>> 	{ "N*"  "N" "sp2" }
>> 	{ "NP"  "N" "sp2" }
>> 	{ "NQ"  "N" "sp2" }
>> 	{ "NB"  "N" "sp2" }
>> 	{ "NC"  "N" "sp2" }
>> 	{ "NT"  "N" "sp3" }
>> 	{ "NY"  "N" "sp2" }
>> 	{ "N3"  "N" "sp3" }
>> 	{ "S"   "S" "sp3" }
>> 	{ "SH"  "S" "sp3" }
>> 	{ "P"   "P" "sp3" }
>> 	{ "LP"  ""  "sp3" }
>> 	{ "EP"  ""  "sp3" }
>> 	{ "F"   "F" "sp3" }
>> 	{ "Cl"  "Cl" "sp3" }
>> 	{ "Br"  "Br" "sp3" }
>> 	{ "I"   "I"  "sp3" }
>> 	{ "F-"   "F" "sp3" }
>> 	{ "Cl-"  "Cl" "sp3" }
>> 	{ "Br-"  "Br" "sp3" }
>> 	{ "I-"   "I"  "sp3" }
>> 	{ "Li+"  "Li"  "sp3" }
>> 	{ "Na+"  "Na"  "sp3" }
>> 	{ "K+"  "K"  "sp3" }
>> 	{ "Rb+"  "Rb"  "sp3" }
>> 	{ "Cs+"  "Cs"  "sp3" }
>> 	{ "Mg+"  "Mg"  "sp3" }
>> # glycam
>> 	{ "OG"  "O" "sp3" }
>> 	{ "OL"  "O" "sp3" }
>> 	{ "AC"  "C" "sp3" }
>> 	{ "EC"  "C" "sp3" }
>> }
>> #
>> #	Load the main parameter set.
>> #
>> parm10 = loadamberparams parm10.dat
Loading parameters: /share/apps/amber/cpu/21/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
>> frcmod14SB = loadamberparams frcmod.ff14SB
Loading parameters: /share/apps/amber/cpu/21/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, nucleic acids
>> #
>> loadOff amino12.lib
Loading library: /share/apps/amber/cpu/21/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: /share/apps/amber/cpu/21/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: /share/apps/amber/cpu/21/dat/leap/lib/aminont12.lib
Loading: ACE
Loading: NALA
Loading: NARG
Loading: NASN
Loading: NASP
Loading: NCYS
Loading: NCYX
Loading: NGLN
Loading: NGLU
Loading: NGLY
Loading: NHID
Loading: NHIE
Loading: NHIP
Loading: NILE
Loading: NLEU
Loading: NLYS
Loading: NMET
Loading: NPHE
Loading: NPRO
Loading: NSER
Loading: NTHR
Loading: NTRP
Loading: NTYR
Loading: NVAL
>> loadOff nucleic12.lib
Loading library: /share/apps/amber/cpu/21/dat/leap/lib/nucleic12.lib
Loading: A
Loading: A3
Loading: A5
Loading: AN
Loading: C
Loading: C3
Loading: C5
Loading: CN
Loading: DA
Loading: DA3
Loading: DA5
Loading: DAN
Loading: DC
Loading: DC3
Loading: DC5
Loading: DCN
Loading: DG
Loading: DG3
Loading: DG5
Loading: DGN
Loading: DT
Loading: DT3
Loading: DT5
Loading: DTN
Loading: G
Loading: G3
Loading: G5
Loading: GN
Loading: OHE
Loading: U
Loading: U3
Loading: U5
Loading: UN
>> #
>> #       Load water and ions
>> # 
>> loadOff atomic_ions.lib
Loading library: /share/apps/amber/cpu/21/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
>> loadOff solvents.lib
Loading library: /share/apps/amber/cpu/21/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
>> 
>> #
>> #	Define the PDB name map for the amino acids and nucleic acids
>> #
>> addPdbResMap {
>>   { 0 "HYP" "NHYP" } { 1 "HYP" "CHYP" }
>>   { 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
>>   { 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
>>   { 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
>>   { 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
>>   { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
>>   { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
>>   { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
>>   { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
>>   { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
>>   { 0 "HID" "NHID" } { 1 "HID" "CHID" }
>>   { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
>>   { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
>>   { 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
>>   { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
>>   { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
>>   { 0 "MET" "NMET" } { 1 "MET" "CMET" }
>>   { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
>>   { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
>>   { 0 "SER" "NSER" } { 1 "SER" "CSER" }
>>   { 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
>>   { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
>>   { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
>>   { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
>>   { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
>>   { 0 "G" "G5"  } { 1 "G" "G3"  } 
>>   { 0 "A" "A5"  } { 1 "A" "A3"  } 
>>   { 0 "C" "C5"  } { 1 "C" "C3"  } 
>>   { 0 "U" "U5"  } { 1 "U" "U3"  } 
>>   { 0 "DG" "DG5"  } { 1 "DG" "DG3"  }  
>>   { 0 "DA" "DA5"  } { 1 "DA" "DA3"  }  
>>   { 0 "DC" "DC5"  } { 1 "DC" "DC3"  }  
>>   { 0 "DT" "DT5"  } { 1 "DT" "DT3"  }  
>> #  some old Amber residue names for RNA:
>>   { 0  "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" }
>>   { 0  "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" }
>>   { 0  "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" }
>>   { 0  "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" }
>> #  some really old Amber residue names, assuming DNA:
>>   { 0 "GUA" "DG5"  } { 1 "GUA" "DG3"  } { "GUA" "DG" }
>>   { 0 "ADE" "DA5"  } { 1 "ADE" "DA3"  } { "ADE" "DA" }
>>   { 0 "CYT" "DC5"  } { 1 "CYT" "DC3"  } { "CYT" "DC" }
>>   { 0 "THY" "DT5"  } { 1 "THY" "DT3"  } { "THY" "DT" }
>> #  uncomment out the following if you have this old style RNA files:
>> # { 0 "GUA" "G5"  } { 1 "GUA" "G3"  } { "GUA" "G" }
>> # { 0 "ADE" "A5"  } { 1 "ADE" "A3"  } { "ADE" "A" }
>> # { 0 "CYT" "C5"  } { 1 "CYT" "C3"  } { "CYT" "C" }
>> # { 0 "URA" "R5"  } { 1 "URA" "R3"  } { "URA" "R" }
>> 
>> }
>> 
>> #  try to be good about reading in really old atom names as well:
>> addPdbAtomMap {
>>   { "O5*" "O5'" }
>>   { "C5*" "C5'" }
>>   { "C4*" "C4'" }
>>   { "O4*" "O4'" }
>>   { "C3*" "C3'" }
>>   { "O3*" "O3'" }
>>   { "C2*" "C2'" }
>>   { "O2*" "O2'" }
>>   { "C1*" "C1'" }
>>   { "C5M" "C7"  }
>>   { "H1*" "H1'" }
>>   { "H2*1" "H2'" }
>>   { "H2*2" "H2''" }
>>   { "H2'1" "H2'" }
>>   { "H2'2" "H2''" }
>>   { "H3*" "H3'" }
>>   { "H4*" "H4'" }
>>   { "H5*1" "H5'" }
>>   { "H5*2" "H5''" }
>>   { "H5'1" "H5'" }
>>   { "H5'2" "H5''" }
>>   { "HO'2" "HO2'" }
>>   { "H5T"  "HO5'" }
>>   { "H3T"  "HO3'" }
>>   { "O1'" "O4'" }
>>   { "OA"  "OP1" }
>>   { "OB"  "OP2" }
>>   { "O1P" "OP1" }
>>   { "O2P" "OP2" }
>> }
>> 
>> #
>> # assume that most often proteins use HIE
>> #
>> NHIS = NHIE
>> HIS = HIE
>> CHIS = CHIE
>> 
> 
> source leaprc.gaff
----- Source: /share/apps/amber/cpu/21/dat/leap/cmd/leaprc.gaff
----- Source of /share/apps/amber/cpu/21/dat/leap/cmd/leaprc.gaff done
>> logFile leap.log
log started: Thu Oct 20 12:11:41 2022

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: /share/apps/amber/cpu/21/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
> 
> source leaprc.water.tip3p
----- Source: /share/apps/amber/cpu/21/dat/leap/cmd/leaprc.water.tip3p
----- Source of /share/apps/amber/cpu/21/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: /share/apps/amber/cpu/21/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
>> loadOff solvents.lib
Loading library: /share/apps/amber/cpu/21/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: /share/apps/amber/cpu/21/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: /share/apps/amber/cpu/21/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: /share/apps/amber/cpu/21/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: /share/apps/amber/cpu/21/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)
>> 
> 
> addAtomTypes {
>         { "M1"  "Mg" "sp3" }
>         { "M2"  "Mg" "sp3" }
>         { "M3"  "Mg" "sp3" }
>         { "Y1"  "O" "sp3" }
>         { "Y2"  "O" "sp3" }
>         { "Y3"  "O" "sp3" }
>         { "Y4"  "O" "sp3" }
>         { "Y5"  "O" "sp3" }
>         { "Y6"  "O" "sp3" }
>         { "Y7"  "O" "sp3" }
>         { "Y8"  "O" "sp3" }
>         { "Y9"  "O" "sp3" }
>         { "Z1"  "O" "sp3" }
>         { "Z2"  "O" "sp3" }
>         { "Z3"  "O" "sp3" }
>         { "Z4"  "O" "sp3" }
>         { "Z5"  "O" "sp3" }
>         { "Z6"  "O" "sp3" }
>         { "Z7"  "O" "sp3" }
> }
> AP1 = loadmol2 AP1.mol2
Loading Mol2 file: ./AP1.mol2
Reading MOLECULE named AP1
> AN1 = loadmol2 AN1.mol2
Loading Mol2 file: ./AN1.mol2
Reading MOLECULE named AN1
> SR1 = loadmol2 SR1.mol2
Loading Mol2 file: ./SR1.mol2
Reading MOLECULE named SR1
> GU1 = loadmol2 GU1.mol2
Loading Mol2 file: ./GU1.mol2
Reading MOLECULE named GU1
> MG1 = loadmol2 MG1.mol2
Loading Mol2 file: ./MG1.mol2
Reading MOLECULE named MG1
> MG2 = loadmol2 MG2.mol2
Loading Mol2 file: ./MG2.mol2
Reading MOLECULE named MG2
> MG3 = loadmol2 MG3.mol2
Loading Mol2 file: ./MG3.mol2
Reading MOLECULE named MG3
> PP1 = loadmol2 PP1.mol2
Loading Mol2 file: ./PP1.mol2
Reading MOLECULE named PP1
> WT1 = loadmol2 WT1.mol2
Loading Mol2 file: ./WT1.mol2
Reading MOLECULE named WT1
> WT2 = loadmol2 WT2.mol2
Loading Mol2 file: ./WT2.mol2
Reading MOLECULE named WT2
> WT3 = loadmol2 WT3.mol2
Loading Mol2 file: ./WT3.mol2
Reading MOLECULE named WT3
> WT4 = loadmol2 WT4.mol2
Loading Mol2 file: ./WT4.mol2
Reading MOLECULE named WT4
> WT5 = loadmol2 WT5.mol2
Loading Mol2 file: ./WT5.mol2
Reading MOLECULE named WT5
> WT6 = loadmol2 WT6.mol2
Loading Mol2 file: ./WT6.mol2
Reading MOLECULE named WT6
> WT7 = loadmol2 WT7.mol2
Loading Mol2 file: ./WT7.mol2
Reading MOLECULE named WT7
> loadamberparams POP.frcmod

/share/apps/amber/cpu/21/bin/teLeap: Fatal Error!
Could not open file POP.frcmod: not found

Exiting LEaP: Errors = 1; Warnings = 0; Notes = 0.
log started: Thu Oct 20 12:12:32 2022

Log file: ./leap.log
>> #
>> # ----- leaprc for loading the ff14SB force field
>> # ----- NOTE: this is designed for PDB format 3!
>> #    Uses frcmod.ff14SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA
>> #
>> #	load atom type hybridizations
>> #
>> addAtomTypes {
>> 	{ "H"   "H" "sp3" }
>> 	{ "HO"  "H" "sp3" }
>> 	{ "HS"  "H" "sp3" }
>> 	{ "H1"  "H" "sp3" }
>> 	{ "H2"  "H" "sp3" }
>> 	{ "H3"  "H" "sp3" }
>> 	{ "H4"  "H" "sp3" }
>> 	{ "H5"  "H" "sp3" }
>> 	{ "HW"  "H" "sp3" }
>> 	{ "HC"  "H" "sp3" }
>> 	{ "HA"  "H" "sp3" }
>> 	{ "HP"  "H" "sp3" }
>> 	{ "HZ"  "H" "sp3" }
>> 	{ "OH"  "O" "sp3" }
>> 	{ "OS"  "O" "sp3" }
>> 	{ "O"   "O" "sp2" }
>> 	{ "O2"  "O" "sp2" }
>> 	{ "OP"  "O" "sp2" }
>> 	{ "OW"  "O" "sp3" }
>> 	{ "CT"  "C" "sp3" }
>> 	{ "CX"  "C" "sp3" }
>> 	{ "C8"  "C" "sp3" }
>> 	{ "2C"  "C" "sp3" }
>> 	{ "3C"  "C" "sp3" }
>> 	{ "CH"  "C" "sp3" }
>> 	{ "CS"  "C" "sp2" }
>> 	{ "C"   "C" "sp2" }
>> 	{ "CO"   "C" "sp2" }
>> 	{ "C*"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CB"  "C" "sp2" }
>> 	{ "CC"  "C" "sp2" }
>> 	{ "CN"  "C" "sp2" }
>> 	{ "CM"  "C" "sp2" }
>> 	{ "CK"  "C" "sp2" }
>> 	{ "CQ"  "C" "sp2" }
>> 	{ "CD"  "C" "sp2" }
>> 	{ "C5"  "C" "sp2" }
>> 	{ "C4"  "C" "sp2" }
>> 	{ "CP"  "C" "sp2" }
>> 	{ "CI"  "C" "sp3" }
>> 	{ "CJ"  "C" "sp2" }
>> 	{ "CW"  "C" "sp2" }
>> 	{ "CV"  "C" "sp2" }
>> 	{ "CR"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CY"  "C" "sp2" }
>> 	{ "C0"  "Ca" "sp3" }
>> 	{ "MG"  "Mg" "sp3" }
>> 	{ "N"   "N" "sp2" }
>> 	{ "NA"  "N" "sp2" }
>> 	{ "N2"  "N" "sp2" }
>> 	{ "N*"  "N" "sp2" }
>> 	{ "NP"  "N" "sp2" }
>> 	{ "NQ"  "N" "sp2" }
>> 	{ "NB"  "N" "sp2" }
>> 	{ "NC"  "N" "sp2" }
>> 	{ "NT"  "N" "sp3" }
>> 	{ "NY"  "N" "sp2" }
>> 	{ "N3"  "N" "sp3" }
>> 	{ "S"   "S" "sp3" }
>> 	{ "SH"  "S" "sp3" }
>> 	{ "P"   "P" "sp3" }
>> 	{ "LP"  ""  "sp3" }
>> 	{ "EP"  ""  "sp3" }
>> 	{ "F"   "F" "sp3" }
>> 	{ "Cl"  "Cl" "sp3" }
>> 	{ "Br"  "Br" "sp3" }
>> 	{ "I"   "I"  "sp3" }
>> 	{ "F-"   "F" "sp3" }
>> 	{ "Cl-"  "Cl" "sp3" }
>> 	{ "Br-"  "Br" "sp3" }
>> 	{ "I-"   "I"  "sp3" }
>> 	{ "Li+"  "Li"  "sp3" }
>> 	{ "Na+"  "Na"  "sp3" }
>> 	{ "K+"  "K"  "sp3" }
>> 	{ "Rb+"  "Rb"  "sp3" }
>> 	{ "Cs+"  "Cs"  "sp3" }
>> 	{ "Mg+"  "Mg"  "sp3" }
>> # glycam
>> 	{ "OG"  "O" "sp3" }
>> 	{ "OL"  "O" "sp3" }
>> 	{ "AC"  "C" "sp3" }
>> 	{ "EC"  "C" "sp3" }
>> }
>> #
>> #	Load the main parameter set.
>> #
>> parm10 = loadamberparams parm10.dat
Loading parameters: /share/apps/amber/cpu/21/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
>> frcmod14SB = loadamberparams frcmod.ff14SB
Loading parameters: /share/apps/amber/cpu/21/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, nucleic acids
>> #
>> loadOff amino12.lib
Loading library: /share/apps/amber/cpu/21/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: /share/apps/amber/cpu/21/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: /share/apps/amber/cpu/21/dat/leap/lib/aminont12.lib
Loading: ACE
Loading: NALA
Loading: NARG
Loading: NASN
Loading: NASP
Loading: NCYS
Loading: NCYX
Loading: NGLN
Loading: NGLU
Loading: NGLY
Loading: NHID
Loading: NHIE
Loading: NHIP
Loading: NILE
Loading: NLEU
Loading: NLYS
Loading: NMET
Loading: NPHE
Loading: NPRO
Loading: NSER
Loading: NTHR
Loading: NTRP
Loading: NTYR
Loading: NVAL
>> loadOff nucleic12.lib
Loading library: /share/apps/amber/cpu/21/dat/leap/lib/nucleic12.lib
Loading: A
Loading: A3
Loading: A5
Loading: AN
Loading: C
Loading: C3
Loading: C5
Loading: CN
Loading: DA
Loading: DA3
Loading: DA5
Loading: DAN
Loading: DC
Loading: DC3
Loading: DC5
Loading: DCN
Loading: DG
Loading: DG3
Loading: DG5
Loading: DGN
Loading: DT
Loading: DT3
Loading: DT5
Loading: DTN
Loading: G
Loading: G3
Loading: G5
Loading: GN
Loading: OHE
Loading: U
Loading: U3
Loading: U5
Loading: UN
>> #
>> #       Load water and ions
>> # 
>> loadOff atomic_ions.lib
Loading library: /share/apps/amber/cpu/21/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
>> loadOff solvents.lib
Loading library: /share/apps/amber/cpu/21/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
>> 
>> #
>> #	Define the PDB name map for the amino acids and nucleic acids
>> #
>> addPdbResMap {
>>   { 0 "HYP" "NHYP" } { 1 "HYP" "CHYP" }
>>   { 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
>>   { 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
>>   { 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
>>   { 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
>>   { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
>>   { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
>>   { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
>>   { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
>>   { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
>>   { 0 "HID" "NHID" } { 1 "HID" "CHID" }
>>   { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
>>   { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
>>   { 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
>>   { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
>>   { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
>>   { 0 "MET" "NMET" } { 1 "MET" "CMET" }
>>   { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
>>   { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
>>   { 0 "SER" "NSER" } { 1 "SER" "CSER" }
>>   { 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
>>   { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
>>   { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
>>   { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
>>   { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
>>   { 0 "G" "G5"  } { 1 "G" "G3"  } 
>>   { 0 "A" "A5"  } { 1 "A" "A3"  } 
>>   { 0 "C" "C5"  } { 1 "C" "C3"  } 
>>   { 0 "U" "U5"  } { 1 "U" "U3"  } 
>>   { 0 "DG" "DG5"  } { 1 "DG" "DG3"  }  
>>   { 0 "DA" "DA5"  } { 1 "DA" "DA3"  }  
>>   { 0 "DC" "DC5"  } { 1 "DC" "DC3"  }  
>>   { 0 "DT" "DT5"  } { 1 "DT" "DT3"  }  
>> #  some old Amber residue names for RNA:
>>   { 0  "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" }
>>   { 0  "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" }
>>   { 0  "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" }
>>   { 0  "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" }
>> #  some really old Amber residue names, assuming DNA:
>>   { 0 "GUA" "DG5"  } { 1 "GUA" "DG3"  } { "GUA" "DG" }
>>   { 0 "ADE" "DA5"  } { 1 "ADE" "DA3"  } { "ADE" "DA" }
>>   { 0 "CYT" "DC5"  } { 1 "CYT" "DC3"  } { "CYT" "DC" }
>>   { 0 "THY" "DT5"  } { 1 "THY" "DT3"  } { "THY" "DT" }
>> #  uncomment out the following if you have this old style RNA files:
>> # { 0 "GUA" "G5"  } { 1 "GUA" "G3"  } { "GUA" "G" }
>> # { 0 "ADE" "A5"  } { 1 "ADE" "A3"  } { "ADE" "A" }
>> # { 0 "CYT" "C5"  } { 1 "CYT" "C3"  } { "CYT" "C" }
>> # { 0 "URA" "R5"  } { 1 "URA" "R3"  } { "URA" "R" }
>> 
>> }
>> 
>> #  try to be good about reading in really old atom names as well:
>> addPdbAtomMap {
>>   { "O5*" "O5'" }
>>   { "C5*" "C5'" }
>>   { "C4*" "C4'" }
>>   { "O4*" "O4'" }
>>   { "C3*" "C3'" }
>>   { "O3*" "O3'" }
>>   { "C2*" "C2'" }
>>   { "O2*" "O2'" }
>>   { "C1*" "C1'" }
>>   { "C5M" "C7"  }
>>   { "H1*" "H1'" }
>>   { "H2*1" "H2'" }
>>   { "H2*2" "H2''" }
>>   { "H2'1" "H2'" }
>>   { "H2'2" "H2''" }
>>   { "H3*" "H3'" }
>>   { "H4*" "H4'" }
>>   { "H5*1" "H5'" }
>>   { "H5*2" "H5''" }
>>   { "H5'1" "H5'" }
>>   { "H5'2" "H5''" }
>>   { "HO'2" "HO2'" }
>>   { "H5T"  "HO5'" }
>>   { "H3T"  "HO3'" }
>>   { "O1'" "O4'" }
>>   { "OA"  "OP1" }
>>   { "OB"  "OP2" }
>>   { "O1P" "OP1" }
>>   { "O2P" "OP2" }
>> }
>> 
>> #
>> # assume that most often proteins use HIE
>> #
>> NHIS = NHIE
>> HIS = HIE
>> CHIS = CHIE
>> 
> 
> source leaprc.gaff
----- Source: /share/apps/amber/cpu/21/dat/leap/cmd/leaprc.gaff
----- Source of /share/apps/amber/cpu/21/dat/leap/cmd/leaprc.gaff done
>> logFile leap.log
log started: Thu Oct 20 12:12:32 2022

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: /share/apps/amber/cpu/21/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
> 
> source leaprc.water.tip3p
----- Source: /share/apps/amber/cpu/21/dat/leap/cmd/leaprc.water.tip3p
----- Source of /share/apps/amber/cpu/21/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: /share/apps/amber/cpu/21/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
>> loadOff solvents.lib
Loading library: /share/apps/amber/cpu/21/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: /share/apps/amber/cpu/21/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: /share/apps/amber/cpu/21/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: /share/apps/amber/cpu/21/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: /share/apps/amber/cpu/21/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)
>> 
> 
> addAtomTypes {
>         { "M1"  "Mg" "sp3" }
>         { "M2"  "Mg" "sp3" }
>         { "M3"  "Mg" "sp3" }
>         { "Y1"  "O" "sp3" }
>         { "Y2"  "O" "sp3" }
>         { "Y3"  "O" "sp3" }
>         { "Y4"  "O" "sp3" }
>         { "Y5"  "O" "sp3" }
>         { "Y6"  "O" "sp3" }
>         { "Y7"  "O" "sp3" }
>         { "Y8"  "O" "sp3" }
>         { "Y9"  "O" "sp3" }
>         { "Z1"  "O" "sp3" }
>         { "Z2"  "O" "sp3" }
>         { "Z3"  "O" "sp3" }
>         { "Z4"  "O" "sp3" }
>         { "Z5"  "O" "sp3" }
>         { "Z6"  "O" "sp3" }
>         { "Z7"  "O" "sp3" }
> }
> AP1 = loadmol2 AP1.mol2
Loading Mol2 file: ./AP1.mol2
Reading MOLECULE named AP1
> AN1 = loadmol2 AN1.mol2
Loading Mol2 file: ./AN1.mol2
Reading MOLECULE named AN1
> SR1 = loadmol2 SR1.mol2
Loading Mol2 file: ./SR1.mol2
Reading MOLECULE named SR1
> GU1 = loadmol2 GU1.mol2
Loading Mol2 file: ./GU1.mol2
Reading MOLECULE named GU1
> MG1 = loadmol2 MG1.mol2
Loading Mol2 file: ./MG1.mol2
Reading MOLECULE named MG1
> MG2 = loadmol2 MG2.mol2
Loading Mol2 file: ./MG2.mol2
Reading MOLECULE named MG2
> MG3 = loadmol2 MG3.mol2
Loading Mol2 file: ./MG3.mol2
Reading MOLECULE named MG3
> PP1 = loadmol2 PP1.mol2
Loading Mol2 file: ./PP1.mol2
Reading MOLECULE named PP1
> WT1 = loadmol2 WT1.mol2
Loading Mol2 file: ./WT1.mol2
Reading MOLECULE named WT1
> WT2 = loadmol2 WT2.mol2
Loading Mol2 file: ./WT2.mol2
Reading MOLECULE named WT2
> WT3 = loadmol2 WT3.mol2
Loading Mol2 file: ./WT3.mol2
Reading MOLECULE named WT3
> WT4 = loadmol2 WT4.mol2
Loading Mol2 file: ./WT4.mol2
Reading MOLECULE named WT4
> WT5 = loadmol2 WT5.mol2
Loading Mol2 file: ./WT5.mol2
Reading MOLECULE named WT5
> WT6 = loadmol2 WT6.mol2
Loading Mol2 file: ./WT6.mol2
Reading MOLECULE named WT6
> WT7 = loadmol2 WT7.mol2
Loading Mol2 file: ./WT7.mol2
Reading MOLECULE named WT7
> loadamberparams POP.frcmod
Loading parameters: ./POP.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
> loadamberparams frcmod.ions1lm_126_tip3p
Loading parameters: /share/apps/amber/cpu/21/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 6OFV_mcpbpy.frcmod
Loading parameters: ./6OFV_mcpbpy.frcmod
Reading force field modification type file (frcmod)
Reading title:
REMARK GOES HERE, THIS FILE IS GENERATED BY MCPB.PY
> mol = loadpdb 6OFV_mcpbpy.pdb
Loading PDB file: ./6OFV_mcpbpy.pdb
Matching PDB residue names to LEaP variables.
Mapped residue ALA, term: Terminal/beginning, seq. number: 0 to: NALA.
Mapped residue ASN, term: Terminal/last, seq. number: 339 to: CASN.

/share/apps/amber/cpu/21/bin/teLeap: Warning!
One sided connection. Residue (AP1) missing connect0 atom.

/share/apps/amber/cpu/21/bin/teLeap: Warning!
One sided connection. Residue (default_name) missing connect1 atom.

/share/apps/amber/cpu/21/bin/teLeap: Warning!
One sided connection. Residue (AN1) missing connect0 atom.

/share/apps/amber/cpu/21/bin/teLeap: Warning!
One sided connection. Residue (default_name) missing connect1 atom.

/share/apps/amber/cpu/21/bin/teLeap: Warning!
One sided connection. Residue (SR1) missing connect0 atom.

/share/apps/amber/cpu/21/bin/teLeap: Warning!
One sided connection. Residue (default_name) missing connect1 atom.

/share/apps/amber/cpu/21/bin/teLeap: Warning!
One sided connection. Residue (GU1) missing connect0 atom.

/share/apps/amber/cpu/21/bin/teLeap: Warning!
One sided connection. Residue (default_name) missing connect1 atom.
  total atoms in file: 5468
> bond mol.84.OD1 mol.341.MG
> bond mol.84.OD2 mol.342.MG
> bond mol.225.OD1 mol.343.MG
> bond mol.229.OG mol.343.MG
> bond mol.233.OE2 mol.343.MG
> bond mol.341.MG mol.344.O2
> bond mol.341.MG mol.345.O
> bond mol.341.MG mol.347.O
> bond mol.341.MG mol.349.O
> bond mol.341.MG mol.350.O
> bond mol.342.MG mol.344.O2
> bond mol.342.MG mol.344.O6
> bond mol.342.MG mol.346.O
> bond mol.342.MG mol.349.O
> bond mol.342.MG mol.351.O
> bond mol.343.MG mol.344.O1
> bond mol.343.MG mol.344.O4
> bond mol.343.MG mol.348.O
> bond mol.83.C mol.84.N
> bond mol.84.C mol.85.N
> bond mol.224.C mol.225.N
> bond mol.225.C mol.226.N
> bond mol.228.C mol.229.N
> bond mol.229.C mol.230.N
> bond mol.232.C mol.233.N
> bond mol.233.C mol.234.N
> savepdb mol 6OFV_dry.pdb
Writing pdb file: 6OFV_dry.pdb

/share/apps/amber/cpu/21/bin/teLeap: Warning!
 Converting N-terminal residue name to PDB format: NALA -> ALA

/share/apps/amber/cpu/21/bin/teLeap: Warning!
 Converting C-terminal residue name to PDB format: CASN -> ASN
> saveamberparm mol 6OFV_dry.prmtop 6OFV_dry.inpcrd
Checking Unit.

/share/apps/amber/cpu/21/bin/teLeap: Warning!
The unperturbed charge of the unit (-10.999998) is not zero.

/share/apps/amber/cpu/21/bin/teLeap: Note.
Ignoring the warning from Unit Checking.

Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.

/share/apps/amber/cpu/21/bin/teLeap: Note.
1-4: angle 5436 5437 duplicates bond ('triangular' bond) or angle ('square' bond)


/share/apps/amber/cpu/21/bin/teLeap: Note.
1-4: angle 5441 5460 duplicates bond ('triangular' bond) or angle ('square' bond)

Building improper torsion parameters.
 total 1224 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
  (Residues lacking connect0/connect1 - 
   these don't have chain types marked:

	res	total affected

	AN1	1
	AP1	1
	CASN	1
	GU1	1
	NALA	1
	PP1	1
	SR1	1
	WT1	1
	WT2	1
	WT3	1
	WT4	1
	WT5	1
	WT6	1
	WT7	1
  )
 (no restraints)
> solvatebox mol TIP3PBOX 10.0
  Solute vdw bounding box:              64.605 53.427 57.449
  Total bounding box for atom centers:  84.605 73.427 77.449
  Solvent unit box:                     18.774 18.774 18.774
The number of boxes:  x= 5  y= 4  z= 5
  Total vdw box size:                   87.721 76.664 80.740 angstroms.
  Volume: 542981.221 A^3 
  Total mass 269294.346 amu,  Density 0.824 g/cc
  Added 12749 residues.
> addions mol Na+ 0
11 Na+ ions required to neutralize.
Adding 11 counter ions to "mol" using 1A grid
Total solute charge:  -11.00  Max atom radius:   2.10
Grid extends from solute vdw + 3.38  to  9.48
Box:
   enclosing:  -40.25 -35.22 -37.29   40.27 34.64 36.82
   sized:			      87.75 92.78 90.71
   edge:        128.00
Resolution:      1.00 Angstrom.
Tree depth: 7
Volume =  3.26% of box, grid points 68432
Solvent present: replacing closest with ion
	 when steric overlaps occur
Calculating grid charges
(Replacing solvent molecule)
Placed Na+ in mol at (21.60, 22.41, 1.06).
(Replacing solvent molecule)
Placed Na+ in mol at (28.87, 11.65, 1.62).
(Replacing solvent molecule)
Placed Na+ in mol at (22.01, -13.91, 7.15).
(Replacing solvent molecule)
Placed Na+ in mol at (-2.10, -21.87, 3.36).
(Replacing solvent molecule)
Placed Na+ in mol at (13.43, 23.52, -0.99).
(Replacing solvent molecule)
Placed Na+ in mol at (24.65, -24.58, -11.00).
(Replacing solvent molecule)
Placed Na+ in mol at (14.09, 14.51, -6.64).
(Replacing solvent molecule)
Placed Na+ in mol at (7.55, -21.34, -12.79).
(Replacing solvent molecule)
Placed Na+ in mol at (27.07, -7.78, 9.76).
(Replacing solvent molecule)
Placed Na+ in mol at (-17.85, 15.70, 3.24).
(Replacing solvent molecule)
Placed Na+ in mol at (25.42, 17.68, 8.63).

Done adding ions.
> addions mol Cl- 0
 0.000002 0 1 0
0 Cl- ion required to neutralize.
Adding 0 counter ions to "mol" using 1A grid
> savepdb mol 6OFV_solv.pdb
Writing pdb file: 6OFV_solv.pdb
   printing CRYST1 record to PDB file with box info

/share/apps/amber/cpu/21/bin/teLeap: Warning!
 Converting N-terminal residue name to PDB format: NALA -> ALA

/share/apps/amber/cpu/21/bin/teLeap: Warning!
 Converting C-terminal residue name to PDB format: CASN -> ASN
> saveamberparm mol 6OFV_solv.prmtop 6OFV_solv.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.

/share/apps/amber/cpu/21/bin/teLeap: Note.
1-4: angle 5436 5437 duplicates bond ('triangular' bond) or angle ('square' bond)


/share/apps/amber/cpu/21/bin/teLeap: Note.
1-4: angle 5441 5460 duplicates bond ('triangular' bond) or angle ('square' bond)

Building improper torsion parameters.
 total 1224 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
  (Residues lacking connect0/connect1 - 
   these don't have chain types marked:

	res	total affected

	AN1	1
	AP1	1
	CASN	1
	GU1	1
	NALA	1
	PP1	1
	SR1	1
	WAT	12738
	WT1	1
	WT2	1
	WT3	1
	WT4	1
	WT5	1
	WT6	1
	WT7	1
  )
 (no restraints)
> quit
	Quit

Exiting LEaP: Errors = 0; Warnings = 13; Notes = 5.
