[gmx-users] output pdb reformatted

[Justin Lemkul]

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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