12 December 2018 1 1K Report

I got an a fatal error "Atom OXT in residue ASP 174 was not found in rtp entry ASP with 9 atoms while sorting atoms." while using pdb2gmx in GROMACS. How could I deal with this OXT atom? What does this OXT atom mean? There supposed to be three oxygen atoms in a ASP residue? And why there are four? Can I just manually delete it?

I am using GROMACS 5.1.4. The PDB file is form pdb bank: 1dat. The part containing OXT is shown below. The command is: gmx pdb2gmx -f 1dat.pdb -o 1dat.gro -water spce -p topol.top

ATOM 1389 N ASP A 174 10.756 5.874 37.839 1.00 57.20 N

ATOM 1390 CA ASP A 174 11.821 6.921 37.802 1.00 56.33 C

ATOM 1391 C ASP A 174 12.548 7.251 39.152 1.00 55.39 C

ATOM 1392 O ASP A 174 11.824 7.735 40.072 1.00 53.97 O

ATOM 1393 CB ASP A 174 11.227 8.235 37.317 1.00 58.62 C

ATOM 1394 CG ASP A 174 12.324 9.362 37.374 1.00 60.87 C

ATOM 1395 OD1 ASP A 174 13.181 9.292 36.404 1.00 59.07 O

ATOM 1396 OD2 ASP A 174 12.269 10.217 38.360 1.00 61.27 O

ATOM 1397 OXT ASP A 174 13.811 7.210 39.231 1.00 52.16 O

TER 1398 ASP A 174

Thanks in advance.

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