[gmx-users] pdb2gmx error

Dries Van Rompaey dries.vanrompaey at gmail.com
Wed Oct 7 20:42:32 CEST 2015

Hi everyone,

I'm getting the following warning when I try to run pdb2gmx on my protein

WARNING: WARNING: Residue 168 named PRO of a molecule in the input file was
mapped to an entry in the topology database, but the atom H used in an
interaction of type dihedral in that entry is not found in the input file.
Perhaps your atom and/or residue naming needs to be fixed.

This warning is only present when I use the AMBER03 forcefield, all other
forcefields seem to work fine. I have tried this with both a structure
without hydrogens as well as a structure with hydrogens added, both with
and without the -ignh flag. I tried looking at the amber03 database files
as well as the amber99sb-ildn database files (amber99sb-ildn works just
fine), but I could not find any reason why this particular residue would be
problematic. pdb2gmx does not find any problems with the other proline
residues in the protein (which look identical), so I am puzzled as to
what's causing this.

The proline residue is:
ATOM   1384  N   PRO A 168     274.650  45.241  24.167  1.00180.63
ATOM   1385  CA  PRO A 168     273.508  44.823  23.370  1.00180.63
ATOM   1386  CD  PRO A 168     275.844  45.381  23.346  1.00180.63
ATOM   1387  CB  PRO A 168     274.071  44.405  22.014  1.00180.63
ATOM   1388  CG  PRO A 168     275.381  45.194  21.892  1.00180.63
ATOM   1389  C   PRO A 168     272.551  43.776  23.888  1.00180.63
ATOM   1390  O   PRO A 168     271.478  43.646  23.304  1.00180.63

Does anyone know what's going on here?

Thanks in advance!

More information about the gromacs.org_gmx-users mailing list