[gmx-users] pdb2gmx error
Dries Van Rompaey
dries.vanrompaey at gmail.com
Wed Oct 7 20:42:32 CEST 2015
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!
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