[gmx-users] Parameters for small molecule

David van der Spoel spoel at xray.bmc.uu.se
Mon Jan 14 12:58:22 CET 2002

On Mon, 14 Jan 2002, Andrew Horsfield wrote:

>I want to perform a simulation using both a small molecule and a large
>protein. I would like to use accurate charges (from an electronic
>structure calculation) for the small molecule. If I do not modify the
>gromacs parameters I get a badly wrong geometry for the small molecule
>when I relax it. So I must refit the bonding parameters, and use these
>special values in the topology file. Is there a simple way to do this for
>a small molecule? I could see 
Did you try the prodrg 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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