[gmx-users] pdb2gmx error

[Dries Van Rompaey]

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" <jalemkul at 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.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!
>>>> --
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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
> http://mackerell.umaryland.edu/~jalemkul
>
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