Pdb2gmx fails to recognize OXT in terminal valine

User discussions
1

GROMACS version: 2025.3
GROMACS modification: No

I am attempting to use pdb2gmx thus:

gmx pdb2gmx -ff amber99sb-ildn -water tip3p -ignh -f 5xn3.cpx.pdb -o cpx -p cpx -i cpx.posre

which generates an error:

Fatal error:
Atom OXT in residue VAL 8 was not found in rtp entry VAL with 16 atoms
while sorting atoms.

This error does not occur on others’ computers.

this OXT residue in terminal VAL is present in other PDB files, and pdb2gmx did NOT throw an error for those. I don’t understand what’s significant about the PDB 5XN3, with the lines in question:

ATOM 3018 OXT GLY A 221 4.920 11.607 -5.875 1.00 0.00 O

ATOM 3142 OXT VAL B 8 2.166 -14.680 32.489 1.00 0.00 O

If I replace atom 3142 with O instead of OXT , pdb2gmx works, but that’s not correct.

Why am I getting this error? Is gromacs not built correctly?

This error also occurs in the newest Gromacs 2026.0

2

Hello, this is almost certainly not a GROMACS internal error but a mismatch between the pdb and force fields. Many forcefields have different residue names for terminal residues, amber ff’s among them. An N-terminal resi will go from being VAL to NVAL and C term will change likewise. This may resolve your atom naming issue, or you may have to check the amber99sb-ildn directory as it may use a different terminal-O naming convention altogether. For instructions on finding that dir see here.