[gmx-users] Full topology from pdf2gmx

[Mark Abraham]

Hi,

Sure, that's what grompp does as part of making a .tpr. The only way to get
a (somewhat) human readable version is to use gmx dump on that .tpr. Tips -
numbering starts from zero, and you probably want to see what's going on
with the smallest system that has the relevant complexity.

Mark

On Thu, Aug 4, 2016 at 6:20 PM Eric Smoll <ericsmoll at gmail.com> wrote:

> Hello Justin,
>
> Thank you for the response. It looks like grompp -pp only expands includes,
> it does not add unspecified force constants to directives (bonds, angles,
> etc.)
>
> Best,
> Eric
>
> On Wed, Aug 3, 2016 at 4:13 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 8/3/16 11:18 AM, Eric Smoll wrote:
> >
> >> Hello GROMACS users,
> >>
> >> Pdb2gmx generates a topology without parameters under directives like
> >> bonds, angles, etc. This is because it references information in the
> >> specified forcefield database. Is it possible to generate a fully
> >> populated
> >> topology with force constants, equilibrium distances, etc.?
> >>
> >>
> > Try grompp -pp.
> >
> > -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
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> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
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