[gmx-users] protein problems (aka why me?)

David spoel at xray.bmc.uu.se
Mon Aug 12 20:26:58 CEST 2002

On Mon, 2002-08-12 at 17:10, David L. Bostick wrote:
> Hi ..
> I did exactly (sort of this) when modelling halorhodopsin.  You need to
> create a residue in the database.  Jeremy Smith had a few papers a while
> back on a model of the retinal moiety.. you may find this a useful guide
> for parameters.
Actually we have done it for bacteriorhodopsin simulations. Topology can
be made without problems, but parameters, in particular charges, are

I've attached the modified parameter files. Charges are from papers by
Tajkhorshid et al.

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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