Atom OXT in residue DTRP 14 was not found in rtp entry DTRP with 24 atoms while sorting atoms

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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.
.

For more information and tips for troubleshooting, please check the GROMACS
website at Errors - Gromacs

Hi
pdb2gmx does not recognize the atoms in DTRP.
First, you can check if DTRP is an entry in residues database of the force field you are using ./charmm36-jul2020.ff/merged.rtp.
Best regards
Alessandra

Yeah it is there

The .rtp entry is not the problem. pdb2gmx doesn’t recognize DTRP as a protein residue. Here’s your hint:

But you have 14 residues. So pdb2gmx thinks DTRP is a separate entity, i.e. not a protein residue, so it applies terminal patching to Ala1 and Leu13, then tries to treat DTRP as a standalone amino acid, hence it does not find OXT in the .rtp entry for it (because that comes from the patch in the .c.tdb file).

The solution is to add DTRP (and any other D-amino acids) to residuetypes.dat, defined as Protein.

Thank you that work but now I am having a different problem

FATAL ERROR-
Residue 1 named ALA of a molecule in the input file was mapped to an entry in topology database, but the atom N used in that entry is not found in input file. Perhaps your atom and residue naming needs to be changed

Please provide the full screen output from pdb2gmx (always do this when reporting such problems). There is no reason that I can see why the N-terminus was previously recognized and now isn’t.

going to rename ./charmm36-jul2020.ff/merged.r2b
Opening force field file ./charmm36-jul2020.ff/merged.r2b
Reading ld14_proa.pdb…
Read ‘’, 99 atoms
Analyzing 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 99 atoms

chain #res #atoms
1 ’ ’ 14 99

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 (99 atoms, 14 residues)
Identified residue ALA1 as a starting terminus.
Identified residue DTRP14 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Start terminus ALA-1: NH3+
End terminus DTRP-14: COO-
Opening force field file ./charmm36-jul2020.ff/merged.arn
Checking for duplicate atoms…
Generating any missing hydrogen atoms and/or adding termini.


Program: gmx pdb2gmx, version 2020.1-Ubuntu-2020.1-1
Source file: src/gromacs/gmxpreprocess/pgutil.cpp (line 130)

Fatal error:
Residue 1 named ALA of a molecule in the input file was mapped
to an entry in the topology database, but the atom N used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.

For more information and tips for troubleshooting, please check the GROMACS
website at Errors - Gromacs

OK, so apparently there is no atom named N in Ala1. It either needs to be renamed (if present but with a different name) or modeled in (if missing).

ALA1 in PDB , there is N in pdb right?
ATOM 1 N ALA 1 7.273 -0.781 1.149 0.00 0.00 PROA
ATOM 2 CA ALA 1 7.162 -0.314 -0.225 0.00 0.00 PROA
ATOM 3 C ALA 1 7.351 1.200 -0.359 0.00 0.00 PROA
ATOM 4 O ALA 1 7.560 1.818 0.627 0.00 0.00 PROA
ATOM 5 CB ALA 1 5.746 -0.689 -0.719 0.00 0.00 PROA
ATOM 6 HA ALA 1 7.904 -0.824 -0.840 0.00 0.00 PROA
ATOM 7 HB1 ALA 1 5.619 -0.356 -1.749 0.00 0.00 PROA
ATOM 8 HB2 ALA 1 5.000 -0.206 -0.088 0.00 0.00 PROA
ATOM 9 HB3 ALA 1 5.618 -1.770 -0.669 0.00 0.00 PROA
ATOM 10 HT1 ALA 1 7.133 -1.841 1.178 0.00 0.00 PROA
ATOM 11 HT2 ALA 1 6.525 -0.306 1.749 0.00 0.00 PROA

So it seems. Sorry, I have no idea why pdb2gmx won’t accept it.

ok, let me try

Thank you