[gmx-users] pdb2gmx error
Justin Lemkul
jalemkul at vt.edu
Thu Oct 15 13:28:58 CEST 2015
On 10/15/15 4:18 AM, Dries Van Rompaey wrote:
> 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).
>
Indeed, it seems that the AMBER03 version of GLY has a bunch of dihedrals
defined that shouldn't be. It also looks like it is the only AMBER force field
that does this, so it's clearly a mistake. I will submit a patch for the 5.1
series. Thanks for digging into this.
-Justin
>
> 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
>>>>>>>>>>
>>>>>>>>>> * Please search the archive at
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>>>>>>>>>> posting!
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>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>>
>>>>>>>>>> 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
>>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>>>> posting!
>>>>>>>
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>>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>> ==================================================
>>>>>
>>>>> 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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>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>
>>>>>
>>> --
>>> ==================================================
>>>
>>> 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!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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>>> send a mail to gmx-users-request at gromacs.org.
>>>
>>
>>
--
==================================================
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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