[gmx-users] pdb2gmx error

[Justin Lemkul]

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" <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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-- 
==================================================

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

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