[gmx-users] pdb2gmx error

Dries Van Rompaey dries.vanrompaey at gmail.com
Thu Oct 8 14:15:46 CEST 2015


I definitely agree that it's odd that the warning only occurs with this
specific residue. I ran a diff against the freshly downloaded AMBER03
files, but they were identical. I also tried running it again with freshly
downloaded amber03 files in the directory.

About the error: pdb2gmx never crashed. It always runs to completion and
mentions that the topology was successfully generated. I only get a warning
during the execution of pdb2gmx.

Thanks for all your help,

Dries



On 8 October 2015 at 13:33, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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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>>>>>>>> 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
>>>>>
>>>>> ==================================================
>>>>> --
>>>>> 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
>>>
>>> ==================================================
>>> --
>>> 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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