[gmx-users] output pdb reformatted

[Alex]

You are absolutely right once again. I've been glancing over that topology,
looking right at what the problem was, and not seeing it. The residue name
column was empty, all atom types went to crap, but because I always grompp
with -maxwarn 10 (for completely unrelated warnings in completely different
simulations) everything seemed okay.

Thanks!

Alex

On Tue, Jul 11, 2017 at 2:40 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/11/17 4:01 PM, Alex wrote:
>
>> Hi all,
>>
>> I have a tiny acetonitrile molecule here. The input pdb prior to EM is
>> this:
>>
>> TITLE     Gromacs Runs On Most of All Computer Systems
>> REMARK    THIS IS A SIMULATION BOX
>> CRYST1   30.000   30.000   30.000  90.00  90.00  90.00 P 1
>> MODEL        1
>> ATOM      1  CT  ACT     1      14.870  14.744  14.594  1.00  0.00
>>    C
>> ATOM      2  HC  ACT     1      15.390  13.760  14.594  1.00  0.00
>>    H
>> ATOM      3  HC  ACT     1      13.769  14.581  14.594  1.00  0.00
>>    H
>> ATOM      4  HC  ACT     1      15.162  15.317  13.685  1.00  0.00
>>    H
>> ATOM      5  CZ  ACT     1      15.253  15.501  15.794  1.00  0.00
>>    C
>> ATOM      6  NZ  ACT     1      15.555  16.097  16.740  1.00  0.00
>>    N
>> TER
>> ENDMDL
>>
>> The output, however, is this:
>>
>> TITLE     Great Red Owns Many ACres of Sand
>> REMARK    THIS IS A SIMULATION BOX
>> CRYST1   30.000   30.000   30.000  90.00  90.00  90.00 P 1           1
>> MODEL        1
>> ATOM      1  1    CT     1      15.013  15.013  14.819  1.00  0.00
>>    C
>> ATOM      2  1    HC     1      14.952  13.831  14.385  1.00  0.00
>>    H
>> ATOM      3  1    HC     1      13.827  14.934  14.400  1.00  0.00
>>    H
>> ATOM      4  1    HC     1      15.140  15.157  13.573  1.00  0.00
>>    H
>> ATOM      5  2    CZ     1      15.821  15.819  16.308  1.00  0.00
>>    C
>> ATOM      6  2    NZ     1      16.401  16.397  17.446  1.00  0.00
>>    N
>> TER
>> ENDMDL
>>
>> Why? I don't think I've seen this happen before, and I'd like to keep the
>> initial format. Any suggestions? My itp is for an ACT residue, which is
>> included in the simulation topology input.
>>
>>
> mdrun gets the residue and atom names from the topology, so a dump of the
> .tpr should show something useful.  It seems like something in the topology
> has gotten broken - atom names becoming numbers, residue name becoming the
> atom names.  Bizarre.  grompp should have complained loudly if there were
> mismatches between coordinates and topology.
>
> -Justin
>
> --
> ==================================================
>
> 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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