[gmx-users] non protein input

[Daan van Aalten]

Hi Lambert

By far the best strategy for generating polymers topologies is to write
"residue" (read: monomer) topologies first (see the .rtp files) and then
use these to generate topologies for oligo/polymers.

However, PRODRG is also an option, as the atom limit on the server is
simply there as a (CPU/memory usage) safeguard. The atom limit can be
changed at the compilation stage and we can provide you with a "large"
version, or would be happy to make the topology for you if you send us
your coordinates.

Daan

On Wed, 25 Aug 2004, Lambert van Eijck wrote:

> Hi,
>
> I'd like to do MD on polymers. The pdb2gmx program complains about unknown
> residues and 'UNK' doesn't seem to  be in the database. I take it, it's
> not usefull to add this type (?).
>
> I'm not sure whether I should try Gromacs on non-proteins. Can someone
> advise me? I've tried the server on the web to convert PDBs to gromacs,
> but there are to many atoms in my models.
>
> Babel will convert into Gromos input, but then I'm not sure how to create
> a .top file, as I just skipped pdb2gmx.
>
> I've searched the mailing list but, couldn't find any references to this
> (basic) questions, except for the web server.
>
> Can I get Gromacs running an MD on polymers?
>
> thanks in advance,
>
> Lambert van Eijck
>
>
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##############################################################################
Dr. Daan van Aalten                    Wellcome Trust Senior Fellow / Reader
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: see WWW page
Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk