[gmx-users] GPCR/any protein modelling

David van der Spoel spoel at xray.bmc.uu.se
Fri Aug 9 13:25:49 CEST 2002

On Fri, 2002-08-09 at 12:42, Chris Shaw wrote:
> Hello All, 
> I am attempting to model a GPCR based on the recently reported crystal structure of rhodopsin. I have done this and are now trying to do some MD on this model. This is where it goes wrong. I have tried to do some MD run on the model as with the "Getting started tutorial". Short runs in water i.e. 50 ps all is fine, however during longer runs i.e. 500 ps (again in water) the secondary structure of the model degrades greatly. Could anyone help me as to where I am going wrong. ANY HELP WOULD BE GREATLY APPRECIATED!!!!
Aren't these membrane proteins?
> Cheers
> Chris
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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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