[gmx-users] GPCR/any protein modelling

Peter C. Lai sirmoo at cowbert.2y.net
Fri Aug 9 17:17:10 CEST 2002

On Fri, Aug 09, 2002 at 11:42:56AM +0100, 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!!!!

1. the solvent as water should work, as the helices are hydrophobic
and should actually pack the helices more, if anything else. 
One would expect the protein to denature if run with an organic 
solvent (e.g. decane). Make sure your helices are oriented correctly
(hydrophobic facing out, hydrophilic facing in).
Of course, I haven't specifically used GROMACS to 
run MD on the helices (see below).

2. How are they falling apart?

3. When I use Discover to run MD on a GPCR, secondary structure falls
apart also (helical elongation and helical destruction in terms of dihedryl violations).
I did this in a vacuum (non-solvated).  THe solution is to add constraints
and fix angles (and/or translation) of the helical alpha carbons.

hope this helps any.

> Cheers
> Chris
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Peter C. Lai
University of Connecticut
Dept. of Molecular and Cell Biology | Undergraduate Research Assistant
Yale University School of Medicine
Center for Medical Informatics | Research Assistant

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