[gmx-users] new molecule rtp and itp files?

[Daan van Aalten]

Hi

If you go to http://davapc1.bioch.dundee.ac.uk/prodrg
you can get your small molecule coordinates and ITP files and in the FAQ
there is a description on how to use these with GROMACS.

cheers

Daan


On Tue, 13 Jan 2004, Milton Taidi Sonoda wrote:

> Could I add the new bonded ff parameters in the rtp file?
> I should say that the new parameter are different from
> the xxxtypes present in the ffxxxbon.itp.
> Do I have to define new xxxtypes for these parameters in
> the ffxxxbon.itp, or the values readed in the rtp are OK?
>
> David wrote:
>
> >On Mon, 2004-01-12 at 20:39, Milton Taidi Sonoda wrote:
> >
> >
> >>Hi
> >>I'm new on GROMACS and I guess I have a very simple question.
> >>If I had to deal with am non-aminoacid new molecule with different
> >>forcefield parameters absent in the ffxxxbon.itp and ffxxxnb.itp files,
> >>do I had to put the new molecule structure in the ffxxx.rtp and
> >>in the same time construct a newmolecule.itp file to include in the
> >>topology file?
> >>
> >>
> >One of those is enough. If you have a new molecule, an itp file is
> >easier. Use prodrg for that. For a protein building block you need to
> >make an rtp entry.
> >
> >
> >
> >>Thank's in advance
> >>Milton Taidi Sonoda
> >>
> >>
> >>
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> >>
>
>
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##############################################################################

Dr. Daan van Aalten                    Wellcome Trust CDA Fellow
Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979
Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764
School of Life Sciences                E-mail: dava at davapc1.bioch.dundee.ac.uk
Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk

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