Hello everyone,
I have a problem with the topology file and coordinate file generated by tleap at the beginning of using AMBER. I imported a single DNA strand, but I don't know why the four phosphate atoms at the 5' end of the first nucleic acid are not recognized. But these four atoms are very important for my subsequent calculations. I would like to ask you how to deal with this?
Thank you and wish you all good luck.
Below is the content of my leap.log file
log started: Tue Mar 18 10:22:28 2025
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/xu/anaconda3/envs/ambertools23/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/xu/anaconda3/envs/ambertools23/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
>> loadamberparams frcmod.DNA.OL15
Loading parameters: /home/xu/anaconda3/envs/ambertools23/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
>
> lig = loadpdb lig1.pdb
Loading PDB file: ./lig1.pdb
Matching PDB residue names to LEaP variables.
Mapped residue DT, term: Terminal/beginning, seq. number: 0 to: DT5.
Mapped residue DC, term: Terminal/last, seq. number: 19 to: DC3.
Created a new atom named: P within residue: .R<DT5 1>
Created a new atom named: OP1 within residue: .R<DT5 1>
Created a new atom named: OP2 within residue: .R<DT5 1>
Created a new atom named: OP3 within residue: .R<DT5 1>
total atoms in file: 412
Leap added 229 missing atoms according to residue templates:
229 H / lone pairs
The file contained 4 atoms not in residue templates
> charge lig
Total unperturbed charge: -19.000000
Total perturbed charge: -19.000000
> saveamberparm lig lig.parm7 lig.rst7
Checking Unit.
/home/xu/anaconda3/envs/ambertools23/bin/teLeap: Warning!
The unperturbed charge of the unit (-19.000000) is not zero.
FATAL: Atom .R<DT5 1>.A<P 31> does not have a type.
FATAL: Atom .R<DT5 1>.A<OP1 32> does not have a type.
FATAL: Atom .R<DT5 1>.A<OP2 33> does not have a type.
FATAL: Atom .R<DT5 1>.A<OP3 34> does not have a type.
/home/xu/anaconda3/envs/ambertools23/bin/teLeap: Fatal Error!
Failed to generate parameters
Exiting LEaP: Errors = 1; Warnings = 1; Notes = 0.
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- application/octet-stream attachment: leap.log
- application/octet-stream attachment: lig1.pdb
Received on Tue Mar 18 2025 - 19:00:02 PDT
