[gmx-users] output pdb reformatted

[Mark Abraham]

Hi,

Please stop doing that. You're risking wasting your own time as well. ;-)

Mark

On Tue, Jul 11, 2017 at 11:52 PM Alex <nedomacho at gmail.com> wrote:

> 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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