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Atom OXT in residue DTRP 14 was not found in rtp entry DTRP with 24 atoms
while sorting atoms.
this is DTRP residue in my pdb
ATOM 193 N DTRP 14 8.258 35.780 -30.239 0.00 0.00 PROA
ATOM 194 CA DTRP 14 8.428 37.208 -30.466 0.00 0.00 PROA
ATOM 195 C DTRP 14 8.289 37.599 -31.941 0.00 0.00 PROA
ATOM 196 O DTRP 14 8.059 36.703 -32.751 0.00 0.00 PROA
ATOM 197 CB DTRP 14 7.348 37.835 -29.553 0.00 0.00 PROA
ATOM 198 CG DTRP 14 7.375 39.331 -29.495 0.00 0.00 PROA
ATOM 199 CD1 DTRP 14 6.496 40.195 -30.144 0.00 0.00 PROA
ATOM 200 CD2 DTRP 14 8.248 40.118 -28.767 0.00 0.00 PROA
ATOM 201 NE1 DTRP 14 6.851 41.442 -29.821 0.00 0.00 PROA
ATOM 202 CE2 DTRP 14 7.892 41.421 -28.996 0.00 0.00 PROA
ATOM 203 CE3 DTRP 14 9.299 39.771 -27.932 0.00 0.00 PROA
ATOM 204 CZ2 DTRP 14 8.564 42.478 -28.408 0.00 0.00 PROA
ATOM 205 CZ3 DTRP 14 9.986 40.823 -27.327 0.00 0.00 PROA
ATOM 206 CH2 DTRP 14 9.625 42.155 -27.562 0.00 0.00 PROA
ATOM 207 OXT DTRP 14 8.415 38.787 -32.232 0.00 0.00 PROA
ATOM 208 HN DTRP 14 8.067 35.290 -31.171 0.00 0.00 PROA
ATOM 209 HA DTRP 14 9.413 37.509 -30.111 0.00 0.00 PROA
ATOM 210 HB1 DTRP 14 6.370 37.526 -29.921 0.00 0.00 PROA
ATOM 211 HB2 DTRP 14 7.494 37.453 -28.542 0.00 0.00 PROA
ATOM 212 HD1 DTRP 14 5.670 39.908 -30.795 0.00 0.00 PROA
ATOM 213 HE1 DTRP 14 6.368 42.328 -30.176 0.00 0.00 PROA
ATOM 214 HE3 DTRP 14 9.573 38.731 -27.757 0.00 0.00 PROA
ATOM 215 HZ2 DTRP 14 8.279 43.513 -28.597 0.00 0.00 PROA
ATOM 216 HZ3 DTRP 14 10.819 40.604 -26.659 0.00 0.00 PROA
ATOM 217 HH2 DTRP 14 10.184 42.954 -27.075 0.00 0.00 PROA
TER
comments by gromacs
nalyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 14 residues with 217 atoms
chain #res #atoms
1 ’ ’ 14 217
All occupancy fields zero. This is probably not an X-Ray structure
Opening force field file ./charmm36-jul2020.ff/atomtypes.atp
Reading residue database… (Charmm36-jul2020)
Opening force field file ./charmm36-jul2020.ff/merged.rtp
Opening force field file ./charmm36-jul2020.ff/merged.hdb
Opening force field file ./charmm36-jul2020.ff/merged.n.tdb
Opening force field file ./charmm36-jul2020.ff/merged.c.tdb
Back Off! I just backed up topol.top to ./#topol.top.2#
Processing chain 1 (217 atoms, 14 residues)
Identified residue ALA1 as a starting terminus.
Identified residue LEU13 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Start terminus ALA-1: NH3+
End terminus LEU-13: COO-
Opening force field file ./charmm36-jul2020.ff/merged.arn
Program: gmx pdb2gmx, version 2020.1-Ubuntu-2020.1-1
Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 745)
Fatal error:
Atom OXT in residue DTRP 14 was not found in rtp entry DTRP with 24 atoms
while sorting atoms.
.
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