[gmx-users] pdb2gmx error
jalemkul at vt.edu
Wed Oct 7 22:59:03 CEST 2015
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 :)
> Kind regards,
> On 7 October 2015 at 20:56, Mark Abraham <mark.j.abraham at gmail.com> wrote:
>> Is it terminal? Are there specbonds in play? What's the GROMACS version?
>> What's your pdb2gmx command line? :-)
>> On Wed, Oct 7, 2015 at 8:43 PM Dries Van Rompaey <
>> dries.vanrompaey at gmail.com>
>>> Hi everyone,
>>> I'm getting the following warning when I try to run pdb2gmx on my protein
>>> WARNING: WARNING: Residue 168 named PRO of a molecule in the input file
>>> 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
>>> 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
>>> 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
>>> ATOM 1385 CA PRO A 168 273.508 44.823 23.370 1.00180.63
>>> ATOM 1386 CD PRO A 168 275.844 45.381 23.346 1.00180.63
>>> ATOM 1387 CB PRO A 168 274.071 44.405 22.014 1.00180.63
>>> ATOM 1388 CG PRO A 168 275.381 45.194 21.892 1.00180.63
>>> ATOM 1389 C PRO A 168 272.551 43.776 23.888 1.00180.63
>>> ATOM 1390 O PRO A 168 271.478 43.646 23.304 1.00180.63
>>> Does anyone know what's going on here?
>>> Thanks in advance!
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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
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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