I definitely agree that it's odd that the warning only occurs with this specific residue. I ran a diff against the freshly downloaded AMBER03 files, but they were identical. I also tried running it again with freshly downloaded amber03 files in the directory.
About the error: pdb2gmx never crashed. It always runs to completion and mentions that the topology was successfully generated. I only get a warning during the execution of pdb2gmx. Thanks for all your help, Dries On 8 October 2015 at 13:33, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 10/8/15 1:54 AM, Dries Van Rompaey wrote: > >> Thanks for the reply Justin. I unfortunately cannot currently disclose the >> files that I'm working on. Based on the info presented, would you say that >> it's an issue with the force field definition or with the actual protein >> topology? I am not planning on using amber03 in my simulations at the >> moment, so this specific warning is not that important, but I can't help >> but wonder if this warning means something is off in the topology. >> >> > Given that error, there is no topology produced, so there's not going to > be a problem with the topology itself. > > I'm sorry to say that without your actual files, there's literally nothing > we can do to diagnose this. You say some prolines work with AMBER03 and > others don't, which makes no sense at all. Either the .rtp is sound or it > isn't. Either it is unmodified (which will work) or someone has tampered > with it and broken it. > > If you're not going to use AMBER03 and the topology is produced with other > force fields, then you know you have a problem with a hacked AMBER03 .rtp > file. It should be very straightforward to simply to a diff against the > unmodified version (which you can get by downloading a fresh GROMACS > tarball if you don't already have it). > > -Justin > > > On 7 October 2015 at 23:05, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> >>> On 10/7/15 5:03 PM, Dries Van Rompaey wrote: >>> >>> 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. >>>> >>>> >>> Without access to all of the files you're looking at, the best I can do >>> is >>> shrug my shoulders because that doesn't make any sense. Some prolines >>> work >>> and one doesn't? That's just not logical. >>> >>> -Justin >>> >>> >>> 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. >>>>> >>>>> >>>>> -- >>> ================================================== >>> >>> 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. >>> >>> > -- > ================================================== > > 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.
