Hi Mark, This is Gromacs 5.0.4. This is a non-terminal residue. The command line used is: gmx pdb2gmx -f complex.pdb -o complex.gro (-ignh) I tried this procedure with and without ignh flag. As far as I know, specbonds is not in play.
Kind regards, Dries On 7 October 2015 at 20:56, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > Is it terminal? Are there specbonds in play? What's the GROMACS version? > What's your pdb2gmx command line? :-) > > Mark > > On Wed, Oct 7, 2015 at 8:43 PM Dries Van Rompaey < > dries.vanromp...@gmail.com> > wrote: > > > 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. > > > -- > 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. > -- 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.
