[gmx-users] Full topology from pdf2gmx

[Mark Abraham]

Hi,

No, indeed there is no tool for that.

But I think for didactic purposes it is also good to have an example
topology file with comments that observe that the role of the files
included above by forcefield.itp is to provide default parameters, which
function as if

#include "forcefield.itp"
; description of what this does, including expressing things like
; [atomtypes]
; type-a type-b function-type distance force-constant
; CT     CA      1             0.14 4.3e5
; which i'm just making up for the example

[moleculetype]
; name   nrexcl
Example 3

[atoms]
1 CT
2 CA

[bonds]
1 2 ; looks up the atom types for 1 and 2, and then the default bond for
those types, so equivalent to
; a b function-type distance force-constant
; 1 2 1             0.14      4.3e5
; but could be over-ridden with explicit parameters if that was useful

Mark

On Thu, Aug 4, 2016 at 6:41 PM Eric Smoll <ericsmoll at gmail.com> wrote:

> Hi Mark,
>
> Thanks for the response.
>
> I am aware of gmx dump. The gromacs forcefield structure is very flexible
> and powerful but it is a bit scattered. I was curious if there was a simple
> way to format the information in a new topology file to provide to
> beginners. This is particularly useful when the project deviates from
> vanilla forcefield parameters.
>
> What I am suggesting can be accomplished by parsing the various files of
> interest with a script but, as you mention, this is reinventing the wheel
> since grompp does exactly that.
>
> It does not seem like there is an existing tool for this. Thanks for the
> help anyway.
>
> Best,
> Eric
>
> On Thu, Aug 4, 2016 at 10:27 AM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > 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
> > > > 20 Penn St.
> > > > Baltimore, MD 21201
> > > >
> > > > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > > > http://mackerell.umaryland.edu/~jalemkul
> > > >
> > > > ==================================================
> > > > --
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