[gmx-users] pdb2gmx error
Dries Van Rompaey
dries.vanrompaey at gmail.com
Thu Oct 15 10:18:14 CEST 2015
I did some more testing, it seems that this only occurs when the PRO
residue is preceded by a glycine. Could this be related to this issue:
http://comments.gmane.org/gmane.science.biology.gromacs.user/72687 ? When I
change the glycine residue to anything else, pdb2gmx works like a charm. I
constructed a simple test system in which I can replicate the error (see
below).
REMARK 99 MOE v2014.09 (Chemical Computing Group Inc.) Thu Oct 15 10:05:39
2015
ATOM 1 N ALA 1 0.268 -1.146 -1.547 1.00 0.00
N1+
ATOM 2 CA ALA 1 0.506 0.327 -1.714 1.00 0.00
C
ATOM 3 CB ALA 1 -0.837 1.004 -1.931 1.00 0.00
C
ATOM 4 C ALA 1 1.226 0.877 -0.480 1.00 0.00
C
ATOM 5 O ALA 1 1.399 0.165 0.509 1.00 0.00
O
ATOM 6 H1 ALA 1 -0.272 -1.324 -0.688 1.00 0.00
H
ATOM 7 H2 ALA 1 -0.224 -1.571 -2.343 1.00 0.00
H
ATOM 8 H3 ALA 1 1.161 -1.641 -1.413 1.00 0.00
H
ATOM 9 HA ALA 1 1.151 0.435 -2.592 1.00 0.00
H
ATOM 10 HB1 ALA 1 -1.364 0.570 -2.788 1.00 0.00
H
ATOM 11 HB2 ALA 1 -1.480 0.906 -1.049 1.00 0.00
H
ATOM 12 HB3 ALA 1 -0.710 2.074 -2.125 1.00 0.00
H
ATOM 13 N GLY 2 1.667 2.171 -0.583 1.00 0.00
N
ATOM 14 CA GLY 2 2.390 2.835 0.493 1.00 0.00
C
ATOM 15 C GLY 2 2.792 4.221 0.005 1.00 0.00
C
ATOM 16 O GLY 2 2.258 4.706 -0.997 1.00 0.00
O
ATOM 17 H GLY 2 1.519 2.744 -1.415 1.00 0.00
H
ATOM 18 HA1 GLY 2 1.730 2.918 1.361 1.00 0.00
H
ATOM 19 HA2 GLY 2 3.269 2.234 0.743 1.00 0.00
H
ATOM 20 N PRO 3 3.764 4.872 0.730 1.00 0.00
N
ATOM 21 CD PRO 3 4.331 4.472 2.006 1.00 0.00
C
ATOM 22 CG PRO 3 4.793 5.786 2.610 1.00 0.00
C
ATOM 23 CB PRO 3 5.270 6.581 1.399 1.00 0.00
C
ATOM 24 CA PRO 3 4.347 6.129 0.260 1.00 0.00
C
ATOM 25 C PRO 3 5.168 5.908 -1.021 1.00 0.00
C
ATOM 26 O PRO 3 5.520 4.796 -1.412 1.00 0.00
O
ATOM 27 HA PRO 3 3.538 6.843 0.069 1.00 0.00
H
ATOM 28 HB1 PRO 3 6.318 6.337 1.188 1.00 0.00
H
ATOM 29 HB2 PRO 3 5.212 7.661 1.568 1.00 0.00
H
ATOM 30 HG1 PRO 3 5.571 5.654 3.367 1.00 0.00
H
ATOM 31 HG2 PRO 3 3.945 6.303 3.076 1.00 0.00
H
ATOM 32 HD1 PRO 3 5.175 3.804 1.803 1.00 0.00
H
ATOM 33 HD2 PRO 3 3.599 3.952 2.629 1.00 0.00
H
ATOM 34 N ALA 4 5.499 7.083 -1.656 1.00 0.00
N
ATOM 35 CA ALA 4 6.262 7.165 -2.905 1.00 0.00
C
ATOM 36 CB ALA 4 5.416 6.725 -4.094 1.00 0.00
C
ATOM 37 C ALA 4 6.738 8.618 -3.177 1.00 0.00
C
ATOM 38 OXT ALA 4 7.513 8.768 -4.161 1.00 0.00
O1-
ATOM 39 O ALA 4 6.290 9.477 -2.354 1.00 0.00
O
ATOM 40 H ALA 4 5.250 8.002 -1.288 1.00 0.00
H
ATOM 41 HA ALA 4 7.137 6.512 -2.806 1.00 0.00
H
ATOM 42 HB1 ALA 4 4.539 7.372 -4.215 1.00 0.00
H
ATOM 43 HB2 ALA 4 5.988 6.759 -5.027 1.00 0.00
H
ATOM 44 HB3 ALA 4 5.053 5.700 -3.965 1.00 0.00
H
TER 45 ALA 4
END
On 8 October 2015 at 14:15, Dries Van Rompaey <dries.vanrompaey at gmail.com>
wrote:
> 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!
>>>>>>>>> --
>>>>>>>>> Gromacs Users mailing list
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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
>>>>>>
>>>>>> * Please search the archive at
>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>>> posting!
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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
>>>>
>>>> * Please search the archive at
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>>>> posting!
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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
>>
>> * Please search the archive at
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>> posting!
>>
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>
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