[gmx-users] pdb2gmx error

[Justin Lemkul]

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.abraham at 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.vanrompaey at 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-request at 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-request at 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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================