[gmx-users] pdb2gmx error
Justin Lemkul
jalemkul at vt.edu
Thu Oct 8 13:34:04 CEST 2015
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 <jalemkul at 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" <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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>>>>>>>
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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
>>
>> ==================================================
>> --
>> Gromacs Users mailing list
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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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