Thanks Justin, that makes sense! I'm wondering why none of the other proline residues triggered that warning though? The same procedure works like a charm with other proteins. On 7 Oct 2015 10:59 pm, "Justin Lemkul" <jalem...@vt.edu> wrote:
> > > On 10/7/15 3:01 PM, Dries Van Rompaey wrote: > >> 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. >> >> > Non-terminal proline does not have an amide H. If your force field .rtp > file claims to use such an atom used in a dihedral (which is what the error > message tells you is happening), find out who altered the file and > reprimand them :) > > -Justin > > 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. >>> >>> > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > 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.
