I did some more testing, it seems that this only occurs when the PRO residue is preceded by a glycine. Could this be related to this issue: http://comments.gmane.org/gmane.science.biology.gromacs.user/72687 ? When I change the glycine residue to anything else, pdb2gmx works like a charm. I constructed a simple test system in which I can replicate the error (see below).
REMARK 99 MOE v2014.09 (Chemical Computing Group Inc.) Thu Oct 15 10:05:39 2015 ATOM 1 N ALA 1 0.268 -1.146 -1.547 1.00 0.00 N1+ ATOM 2 CA ALA 1 0.506 0.327 -1.714 1.00 0.00 C ATOM 3 CB ALA 1 -0.837 1.004 -1.931 1.00 0.00 C ATOM 4 C ALA 1 1.226 0.877 -0.480 1.00 0.00 C ATOM 5 O ALA 1 1.399 0.165 0.509 1.00 0.00 O ATOM 6 H1 ALA 1 -0.272 -1.324 -0.688 1.00 0.00 H ATOM 7 H2 ALA 1 -0.224 -1.571 -2.343 1.00 0.00 H ATOM 8 H3 ALA 1 1.161 -1.641 -1.413 1.00 0.00 H ATOM 9 HA ALA 1 1.151 0.435 -2.592 1.00 0.00 H ATOM 10 HB1 ALA 1 -1.364 0.570 -2.788 1.00 0.00 H ATOM 11 HB2 ALA 1 -1.480 0.906 -1.049 1.00 0.00 H ATOM 12 HB3 ALA 1 -0.710 2.074 -2.125 1.00 0.00 H ATOM 13 N GLY 2 1.667 2.171 -0.583 1.00 0.00 N ATOM 14 CA GLY 2 2.390 2.835 0.493 1.00 0.00 C ATOM 15 C GLY 2 2.792 4.221 0.005 1.00 0.00 C ATOM 16 O GLY 2 2.258 4.706 -0.997 1.00 0.00 O ATOM 17 H GLY 2 1.519 2.744 -1.415 1.00 0.00 H ATOM 18 HA1 GLY 2 1.730 2.918 1.361 1.00 0.00 H ATOM 19 HA2 GLY 2 3.269 2.234 0.743 1.00 0.00 H ATOM 20 N PRO 3 3.764 4.872 0.730 1.00 0.00 N ATOM 21 CD PRO 3 4.331 4.472 2.006 1.00 0.00 C ATOM 22 CG PRO 3 4.793 5.786 2.610 1.00 0.00 C ATOM 23 CB PRO 3 5.270 6.581 1.399 1.00 0.00 C ATOM 24 CA PRO 3 4.347 6.129 0.260 1.00 0.00 C ATOM 25 C PRO 3 5.168 5.908 -1.021 1.00 0.00 C ATOM 26 O PRO 3 5.520 4.796 -1.412 1.00 0.00 O ATOM 27 HA PRO 3 3.538 6.843 0.069 1.00 0.00 H ATOM 28 HB1 PRO 3 6.318 6.337 1.188 1.00 0.00 H ATOM 29 HB2 PRO 3 5.212 7.661 1.568 1.00 0.00 H ATOM 30 HG1 PRO 3 5.571 5.654 3.367 1.00 0.00 H ATOM 31 HG2 PRO 3 3.945 6.303 3.076 1.00 0.00 H ATOM 32 HD1 PRO 3 5.175 3.804 1.803 1.00 0.00 H ATOM 33 HD2 PRO 3 3.599 3.952 2.629 1.00 0.00 H ATOM 34 N ALA 4 5.499 7.083 -1.656 1.00 0.00 N ATOM 35 CA ALA 4 6.262 7.165 -2.905 1.00 0.00 C ATOM 36 CB ALA 4 5.416 6.725 -4.094 1.00 0.00 C ATOM 37 C ALA 4 6.738 8.618 -3.177 1.00 0.00 C ATOM 38 OXT ALA 4 7.513 8.768 -4.161 1.00 0.00 O1- ATOM 39 O ALA 4 6.290 9.477 -2.354 1.00 0.00 O ATOM 40 H ALA 4 5.250 8.002 -1.288 1.00 0.00 H ATOM 41 HA ALA 4 7.137 6.512 -2.806 1.00 0.00 H ATOM 42 HB1 ALA 4 4.539 7.372 -4.215 1.00 0.00 H ATOM 43 HB2 ALA 4 5.988 6.759 -5.027 1.00 0.00 H ATOM 44 HB3 ALA 4 5.053 5.700 -3.965 1.00 0.00 H TER 45 ALA 4 END On 8 October 2015 at 14:15, Dries Van Rompaey <dries.vanromp...@gmail.com> wrote: > 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.
