log started: Wed May 3 19:25:18 2017 Log file: ./leap.log >> # >> # ----- NOTE: this is designed for PDB format 3! >> # Uses ff99bsc0+OL15 for DNA >> # (ff99): Wang et al. J. Comp. Chem. 21: 1049, 2000 >> # (bsc0): Perez et al. Biophys J. 92: 3817, 2007 >> # (OL15): Zgarbova et al. JCTC 11: 5723, 2015 >> # 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" } >> { "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" } >> >> } >> >> # 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" } >> } >> >> # >> # 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: //home/luna.kuleuven.be/u0111760/amber/amber16/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 Loading parameters: //home/luna.kuleuven.be/u0111760/amber/amber16/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA >> loadamberparams frcmod.DNA.OL15 Loading parameters: //home/luna.kuleuven.be/u0111760/amber/amber16/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 > > > foo = sequence {DT5 DT DT3} Sequence: DT5 Sequence: DT Joining DT5 - DT Sequence: DT3 Joining DT - DT3 > > savePdb foo TTT.pdb Writing pdb file: TTT.pdb > saveAmberParm foo TTT.prmtop TTT.inpcrd Checking Unit. WARNING: The unperturbed charge of the unit: -2.000000 is not zero. -- ignoring the warning. Building topology. Building atom parameters. For atom: .R.A Could not find vdW (or other) parameters for type: HO For atom: .R.A Could not find vdW (or other) parameters for type: OH For atom: .R.A Could not find vdW (or other) parameters for type: H1 For atom: .R.A Could not find vdW (or other) parameters for type: H1 For atom: .R.A Could not find vdW (or other) parameters for type: CT For atom: .R.A Could not find vdW (or other) parameters for type: H1 For atom: .R.A Could not find vdW (or other) parameters for type: OS For atom: .R.A Could not find vdW (or other) parameters for type: CT For atom: .R.A Could not find vdW (or other) parameters for type: H2 For atom: .R.A Could not find vdW (or other) parameters for type: N* For atom: .R.A Could not find vdW (or other) parameters for type: CM For atom: .R.A
Could not find vdW (or other) parameters for type: H4 For atom: .R.A Could not find vdW (or other) parameters for type: CM For atom: .R.A Could not find vdW (or other) parameters for type: CT For atom: .R.A Could not find vdW (or other) parameters for type: HC For atom: .R.A Could not find vdW (or other) parameters for type: HC For atom: .R.A Could not find vdW (or other) parameters for type: HC For atom: .R.A Could not find vdW (or other) parameters for type: C For atom: .R.A Could not find vdW (or other) parameters for type: O For atom: .R.A Could not find vdW (or other) parameters for type: NA For atom: .R.A

Could not find vdW (or other) parameters for type: H For atom: .R.A Could not find vdW (or other) parameters for type: C For atom: .R.A Could not find vdW (or other) parameters for type: O For atom: .R.A Could not find vdW (or other) parameters for type: H1 For atom: .R.A Could not find vdW (or other) parameters for type: CT For atom: .R.A Could not find vdW (or other) parameters for type: HC For atom: .R.A Could not find vdW (or other) parameters for type: HC For atom: .R.A Could not find vdW (or other) parameters for type: OS For atom: .R
.A

Could not find vdW (or other) parameters for type: P For atom: .R

.A Could not find vdW (or other) parameters for type: O2 For atom: .R
.A Could not find vdW (or other) parameters for type: O2 For atom: .R
.A Could not find vdW (or other) parameters for type: OS For atom: .R
.A Could not find vdW (or other) parameters for type: H1 For atom: .R
.A Could not find vdW (or other) parameters for type: H1 For atom: .R
.A Could not find vdW (or other) parameters for type: CT For atom: .R
.A Could not find vdW (or other) parameters for type: H1 For atom: .R
.A Could not find vdW (or other) parameters for type: OS For atom: .R
.A Could not find vdW (or other) parameters for type: CT For atom: .R
.A Could not find vdW (or other) parameters for type: H2 For atom: .R
.A Could not find vdW (or other) parameters for type: N* For atom: .R
.A Could not find vdW (or other) parameters for type: CM For atom: .R
.A
Could not find vdW (or other) parameters for type: H4 For atom: .R
.A Could not find vdW (or other) parameters for type: CM For atom: .R
.A Could not find vdW (or other) parameters for type: CT For atom: .R
.A Could not find vdW (or other) parameters for type: HC For atom: .R
.A Could not find vdW (or other) parameters for type: HC For atom: .R
.A Could not find vdW (or other) parameters for type: HC For atom: .R
.A Could not find vdW (or other) parameters for type: C For atom: .R
.A Could not find vdW (or other) parameters for type: O For atom: .R
.A Could not find vdW (or other) parameters for type: NA For atom: .R
.A

Could not find vdW (or other) parameters for type: H For atom: .R
.A Could not find vdW (or other) parameters for type: C For atom: .R
.A Could not find vdW (or other) parameters for type: O For atom: .R
.A Could not find vdW (or other) parameters for type: H1 For atom: .R
.A Could not find vdW (or other) parameters for type: CT For atom: .R
.A Could not find vdW (or other) parameters for type: HC For atom: .R
.A Could not find vdW (or other) parameters for type: HC For atom: .R
.A Could not find vdW (or other) parameters for type: OS For atom: .R.A

Could not find vdW (or other) parameters for type: P For atom: .R.A Could not find vdW (or other) parameters for type: O2 For atom: .R.A Could not find vdW (or other) parameters for type: O2 For atom: .R.A Could not find vdW (or other) parameters for type: OS For atom: .R.A Could not find vdW (or other) parameters for type: H1 For atom: .R.A Could not find vdW (or other) parameters for type: H1 For atom: .R.A Could not find vdW (or other) parameters for type: CT For atom: .R.A Could not find vdW (or other) parameters for type: H1 For atom: .R.A Could not find vdW (or other) parameters for type: OS For atom: .R.A Could not find vdW (or other) parameters for type: CT For atom: .R.A Could not find vdW (or other) parameters for type: H2 For atom: .R.A Could not find vdW (or other) parameters for type: N* For atom: .R.A Could not find vdW (or other) parameters for type: CM For atom: .R.A

Could not find vdW (or other) parameters for type: H4 For atom: .R.A Could not find vdW (or other) parameters for type: CM For atom: .R.A Could not find vdW (or other) parameters for type: CT For atom: .R.A Could not find vdW (or other) parameters for type: HC For atom: .R.A Could not find vdW (or other) parameters for type: HC For atom: .R.A Could not find vdW (or other) parameters for type: HC For atom: .R.A Could not find vdW (or other) parameters for type: C For atom: .R.A Could not find vdW (or other) parameters for type: O For atom: .R.A Could not find vdW (or other) parameters for type: NA For atom: .R.A

Could not find vdW (or other) parameters for type: H For atom: .R.A Could not find vdW (or other) parameters for type: C For atom: .R.A Could not find vdW (or other) parameters for type: O For atom: .R.A Could not find vdW (or other) parameters for type: H1 For atom: .R.A Could not find vdW (or other) parameters for type: CT For atom: .R.A Could not find vdW (or other) parameters for type: HC For atom: .R.A Could not find vdW (or other) parameters for type: HC For atom: .R.A Could not find vdW (or other) parameters for type: OH For atom: .R.A Could not find vdW (or other) parameters for type: HO Parameter file was not saved. > quit Quit