-I: Adding /apps/scratch/compile/amber24/dat/leap/prep to search path. -I: Adding /apps/scratch/compile/amber24/dat/leap/lib to search path. -I: Adding /apps/scratch/compile/amber24/dat/leap/parm to search path. -I: Adding /apps/scratch/compile/amber24/dat/leap/cmd to search path. -f: Source tleap.in. Welcome to LEaP! (no leaprc in search path) Sourcing: ./tleap.in ----- Source: /apps/scratch/compile/amber24/dat/leap/cmd/leaprc.DNA.bsc1 ----- Source of /apps/scratch/compile/amber24/dat/leap/cmd/leaprc.DNA.bsc1 done Log file: ./leap.log Loading parameters: /apps/scratch/compile/amber24/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA Loading library: /apps/scratch/compile/amber24/dat/leap/lib/parmBSC1.lib Loading parameters: /apps/scratch/compile/amber24/dat/leap/parm/frcmod.parmbsc1 Reading force field modification type file (frcmod) Reading title: Parmbsc1 force-field for DNA ----- Source: /apps/scratch/compile/amber24/dat/leap/cmd/leaprc.DNA.OL15 ----- Source of /apps/scratch/compile/amber24/dat/leap/cmd/leaprc.DNA.OL15 done Log file: ./leap.log Substituting map 0DG -> DG5 for 0DG -> DG5 Substituting map 1DG -> DG3 for 1DG -> DG3 Substituting map 0DA -> DA5 for 0DA -> DA5 Substituting map 1DA -> DA3 for 1DA -> DA3 Substituting map 0DC -> DC5 for 0DC -> DC5 Substituting map 1DC -> DC3 for 1DC -> DC3 Substituting map 0DT -> DT5 for 0DT -> DT5 Substituting map 1DT -> DT3 for 1DT -> DT3 Substituting map 0GUA -> DG5 for 0GUA -> DG5 Substituting map 1GUA -> DG3 for 1GUA -> DG3 Substituting map GUA -> DG for GUA -> DG Substituting map 0ADE -> DA5 for 0ADE -> DA5 Substituting map 1ADE -> DA3 for 1ADE -> DA3 Substituting map ADE -> DA for ADE -> DA Substituting map 0CYT -> DC5 for 0CYT -> DC5 Substituting map 1CYT -> DC3 for 1CYT -> DC3 Substituting map CYT -> DC for CYT -> DC Substituting map 0THY -> DT5 for 0THY -> DT5 Substituting map 1THY -> DT3 for 1THY -> DT3 Substituting map THY -> DT for THY -> DT Substituting map O5* -> O5' for O5* -> O5' Substituting map C5* -> C5' for C5* -> C5' Substituting map C4* -> C4' for C4* -> C4' Substituting map O4* -> O4' for O4* -> O4' Substituting map C3* -> C3' for C3* -> C3' Substituting map O3* -> O3' for O3* -> O3' Substituting map C2* -> C2' for C2* -> C2' Substituting map O2* -> O2' for O2* -> O2' Substituting map C1* -> C1' for C1* -> C1' Substituting map C5M -> C7 for C5M -> C7 Substituting map H1* -> H1' for H1* -> H1' Substituting map H2*1 -> H2' for H2*1 -> H2' Substituting map H2*2 -> H2'' for H2*2 -> H2'' Substituting map H2'1 -> H2' for H2'1 -> H2' Substituting map H2'2 -> H2'' for H2'2 -> H2'' Substituting map 'H2' -> H2'' for 'H2' -> H2'' Substituting map H3* -> H3' for H3* -> H3' Substituting map H4* -> H4' for H4* -> H4' Substituting map H5*1 -> H5' for H5*1 -> H5' Substituting map H5*2 -> H5'' for H5*2 -> H5'' Substituting map H5'1 -> H5' for H5'1 -> H5' Substituting map H5'2 -> H5'' for H5'2 -> H5'' Substituting map 'H5' -> H5'' for 'H5' -> H5'' Substituting map HO'2 -> HO2' for HO'2 -> HO2' Substituting map H5T -> HO5' for H5T -> HO5' Substituting map H3T -> HO3' for H3T -> HO3' Substituting map O1' -> O4' for O1' -> O4' Substituting map OA -> OP1 for OA -> OP1 Substituting map OB -> OP2 for OB -> OP2 Substituting map O1P -> OP1 for O1P -> OP1 Substituting map O2P -> OP2 for O2P -> OP2 Loading library: /apps/scratch/compile/amber24/dat/leap/lib/DNA.OL15.lib /apps/scratch/compile/amber24/bin/teLeap: Note. Skipping parm10.dat: already loaded Loading parameters: /apps/scratch/compile/amber24/dat/leap/parm/frcmod.DNA.OL15 Reading force field modification type file (frcmod) Reading title: OL15 force field for DNA (99bsc0-betaOL1-eps-zetaOL1-chiOL4) see http://ffol.upol.cz ----- Source: /apps/scratch/compile/amber24/dat/leap/cmd/leaprc.gaff ----- Source of /apps/scratch/compile/amber24/dat/leap/cmd/leaprc.gaff done Log file: ./leap.log Loading parameters: /apps/scratch/compile/amber24/dat/leap/parm/gaff.dat Reading title: AMBER General Force Field for organic molecules (Version 1.81, May 2017) ----- Source: /apps/scratch/compile/amber24/dat/leap/cmd/leaprc.gaff2 ----- Source of /apps/scratch/compile/amber24/dat/leap/cmd/leaprc.gaff2 done Log file: ./leap.log Loading parameters: /apps/scratch/compile/amber24/dat/leap/parm/gaff2.dat Reading title: AMBER General Force Field for organic molecules (Version 2.2.20, March 2021) Loading Mol2 file: ./esp.mol2 Reading MOLECULE named MOL DA DA3 DA5 DAN DC DC3 DC5 DCN DG DG3 DG5 DGN DT DT3 DT5 DTN MOL gaff Checking 'MOL'.... Checking parameters for unit 'MOL'. Checking for bond parameters. Checking for angle parameters. /apps/scratch/compile/amber24/bin/teLeap: Error! Could not find angle parameter for atom types: o - p3 - os for atom O1 at position -3.028000, -2.260000, 1.553000, atom P1 at position -2.521000, -1.721000, 0.281000, and atom O3 at position -3.395000, -0.527000, -0.304000. /apps/scratch/compile/amber24/bin/teLeap: Error! Could not find angle parameter for atom types: o - p3 - os for atom O2 at position -1.455000, -2.224000, -0.617000, atom P1 at position -2.521000, -1.721000, 0.281000, and atom O3 at position -3.395000, -0.527000, -0.304000. /apps/scratch/compile/amber24/bin/teLeap: Warning! There are missing parameters. Unit is OK. Loading parameters: ./esp.frcmod Reading force field modification type file (frcmod) Reading title: Remark line goes here Checking 'MOL'.... Checking parameters for unit 'MOL'. Checking for bond parameters. Checking for angle parameters. Unit is OK. Building topology. Building atom parameters. Checking Unit. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. total 7 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 MOL 1 ) (no restraints) Quit Exiting LEaP: Errors = 2; Warnings = 1; Notes = 1. > { "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" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "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" } >> } >> # >> # Define the PDB name map for the nucleic acids >> # >> addPdbResMap { >> { 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 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" } >> >> } Substituting map 0DG -> DG5 for 0DG -> DG5 Substituting map 1DG -> DG3 for 1DG -> DG3 Substituting map 0DA -> DA5 for 0DA -> DA5 Substituting map 1DA -> DA3 for 1DA -> DA3 Substituting map 0DC -> DC5 for 0DC -> DC5 Substituting map 1DC -> DC3 for 1DC -> DC3 Substituting map 0DT -> DT5 for 0DT -> DT5 Substituting map 1DT -> DT3 for 1DT -> DT3 Substituting map 0GUA -> DG5 for 0GUA -> DG5 Substituting map 1GUA -> DG3 for 1GUA -> DG3 Substituting map GUA -> DG for GUA -> DG Substituting map 0ADE -> DA5 for 0ADE -> DA5 Substituting map 1ADE -> DA3 for 1ADE -> DA3 Substituting map ADE -> DA for ADE -> DA Substituting map 0CYT -> DC5 for 0CYT -> DC5 Substituting map 1CYT -> DC3 for 1CYT -> DC3 Substituting map CYT -> DC for CYT -> DC Substituting map 0THY -> DT5 for 0THY -> DT5 Substituting map 1THY -> DT3 for 1THY -> DT3 Substituting map THY -> DT for THY -> DT >> >> # 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''" } >> { "'H2'" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "'H5'" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } Substituting map O5* -> O5' for O5* -> O5' Substituting map C5* -> C5' for C5* -> C5' Substituting map C4* -> C4' for C4* -> C4' Substituting map O4* -> O4' for O4* -> O4' Substituting map C3* -> C3' for C3* -> C3' Substituting map O3* -> O3' for O3* -> O3' Substituting map C2* -> C2' for C2* -> C2' Substituting map O2* -> O2' for O2* -> O2' Substituting map C1* -> C1' for C1* -> C1' Substituting map C5M -> C7 for C5M -> C7 Substituting map H1* -> H1' for H1* -> H1' Substituting map H2*1 -> H2' for H2*1 -> H2' Substituting map H2*2 -> H2'' for H2*2 -> H2'' Substituting map H2'1 -> H2' for H2'1 -> H2' Substituting map H2'2 -> H2'' for H2'2 -> H2'' Substituting map 'H2' -> H2'' for 'H2' -> H2'' Substituting map H3* -> H3' for H3* -> H3' Substituting map H4* -> H4' for H4* -> H4' Substituting map H5*1 -> H5' for H5*1 -> H5' Substituting map H5*2 -> H5'' for H5*2 -> H5'' Substituting map H5'1 -> H5' for H5'1 -> H5' Substituting map H5'2 -> H5'' for H5'2 -> H5'' Substituting map 'H5' -> H5'' for 'H5' -> H5'' Substituting map HO'2 -> HO2' for HO'2 -> HO2' Substituting map H5T -> HO5' for H5T -> HO5' Substituting map H3T -> HO3' for H3T -> HO3' Substituting map O1' -> O4' for O1' -> O4' Substituting map OA -> OP1 for OA -> OP1 Substituting map OB -> OP2 for OB -> OP2 Substituting map O1P -> OP1 for O1P -> OP1 Substituting map O2P -> OP2 for O2P -> OP2 >> >> # >> # Load the OL15 force field for DNA >> # >> >> addAtomTypes { >> { "CJ" "C" "sp3" } >> { "C1" "C" "sp2" } >> { "C2" "C" "sp2" } >> { "C7" "C" "sp3" } >> } >> >> loadoff DNA.OL15.lib Loading library: /apps/scratch/compile/amber24/dat/leap/lib/DNA.OL15.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 >> parm10 = loadamberparams parm10.dat /apps/scratch/compile/amber24/bin/teLeap: Note. Skipping parm10.dat: already loaded >> loadamberparams frcmod.DNA.OL15 Loading parameters: /apps/scratch/compile/amber24/dat/leap/parm/frcmod.DNA.OL15 Reading force field modification type file (frcmod) Reading title: OL15 force field for DNA (99bsc0-betaOL1-eps-zetaOL1-chiOL4) see http://ffol.upol.cz > > source leaprc.gaff ----- Source: /apps/scratch/compile/amber24/dat/leap/cmd/leaprc.gaff ----- Source of /apps/scratch/compile/amber24/dat/leap/cmd/leaprc.gaff done >> logFile leap.log log started: Wed Aug 7 12:44:37 2024 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: /apps/scratch/compile/amber24/dat/leap/parm/gaff.dat Reading title: AMBER General Force Field for organic molecules (Version 1.81, May 2017) > > source leaprc.gaff2 ----- Source: /apps/scratch/compile/amber24/dat/leap/cmd/leaprc.gaff2 ----- Source of /apps/scratch/compile/amber24/dat/leap/cmd/leaprc.gaff2 done >> logFile leap.log log started: Wed Aug 7 12:44:37 2024 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" } >> { "c5" "C" "sp3" } >> { "c6" "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" } >> { "cs" "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" } >> { "n5" "N" "sp3" } >> { "n6" "N" "sp3" } >> { "n7" "N" "sp3" } >> { "n8" "N" "sp3" } >> { "n9" "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" } >> { "ns" "N" "sp2" } >> { "nt" "N" "sp2" } >> { "nu" "N" "sp2" } >> { "nv" "N" "sp2" } >> { "nx" "N" "sp3" } >> { "ny" "N" "sp3" } >> { "nz" "N" "sp3" } >> { "n+" "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 gaff2.dat Loading parameters: /apps/scratch/compile/amber24/dat/leap/parm/gaff2.dat Reading title: AMBER General Force Field for organic molecules (Version 2.2.20, March 2021) > > > MOL = loadmol2 esp.mol2 Loading Mol2 file: ./esp.mol2 Reading MOLECULE named MOL > list DA DA3 DA5 DAN DC DC3 DC5 DCN DG DG3 DG5 DGN DT DT3 DT5 DTN MOL gaff > check MOL Checking 'MOL'.... Checking parameters for unit 'MOL'. Checking for bond parameters. Checking for angle parameters. /apps/scratch/compile/amber24/bin/teLeap: Error! Could not find angle parameter for atom types: o - p3 - os for atom O1 at position -3.028000, -2.260000, 1.553000, atom P1 at position -2.521000, -1.721000, 0.281000, and atom O3 at position -3.395000, -0.527000, -0.304000. /apps/scratch/compile/amber24/bin/teLeap: Error! Could not find angle parameter for atom types: o - p3 - os for atom O2 at position -1.455000, -2.224000, -0.617000, atom P1 at position -2.521000, -1.721000, 0.281000, and atom O3 at position -3.395000, -0.527000, -0.304000. /apps/scratch/compile/amber24/bin/teLeap: Warning! There are missing parameters. Unit is OK. > loadamberparams esp.frcmod Loading parameters: ./esp.frcmod Reading force field modification type file (frcmod) Reading title: Remark line goes here > check MOL Checking 'MOL'.... Checking parameters for unit 'MOL'. Checking for bond parameters. Checking for angle parameters. Unit is OK. > saveoff MOL MOL.lib Saving MOL. Building topology. Building atom parameters. > saveamberparm MOL esp.prmtop esp.inpcrd Checking Unit. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. total 7 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 MOL 1 ) (no restraints) > Quit Quit Exiting LEaP: Errors = 2; Warnings = 1; Notes = 1.