Hi everyone, I'm getting the following warning when I try to run pdb2gmx on my protein structure:
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 N ATOM 1385 CA PRO A 168 273.508 44.823 23.370 1.00180.63 C ATOM 1386 CD PRO A 168 275.844 45.381 23.346 1.00180.63 C ATOM 1387 CB PRO A 168 274.071 44.405 22.014 1.00180.63 C ATOM 1388 CG PRO A 168 275.381 45.194 21.892 1.00180.63 C ATOM 1389 C PRO A 168 272.551 43.776 23.888 1.00180.63 C ATOM 1390 O PRO A 168 271.478 43.646 23.304 1.00180.63 O Does anyone know what's going on here? Thanks in advance! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.