[gmx-users] Using GROMACS with small molecules

David van der Spoel spoel at xray.bmc.uu.se
Sun Dec 9 17:55:18 CET 2001

On Sun, 9 Dec 2001, Daan van Aalten wrote:

>non-protein/dna small molecules. However, you can automatically generate
>topologies for almost any small molecule made up of H,C,N,O,P,S,F,Cl,Br,I
>with PRODRG, see
>You mention you want to include metals, which PRODRG currently
>does not support. You could however, fake things by replacing your metals
>with P,C or S and then altering values for non-bonded parameters later by
I would like to urge you to search the literature for appropriate force
field parameters, since this is crucial! I am pretty sure many similar
molecules have been studied by force field methods. If you don't find what
you are looking for, you could try the computational chemistry list
(www.ccl.net). If you succeed in building a molecular topology with good
force field, please upload your topology to the GROMACS web server.

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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