[gmx-users] conformational study of a dual domain protein

David spoel at xray.bmc.uu.se
Fri Sep 27 21:10:35 CEST 2002

On Fri, 2002-09-27 at 23:40, olivier walker wrote:
> Hi all,
> Thanks to David for his answer in the CCL mailing list.
>   I'm studying a dual domain protein and I would like to generate all 
> possible conformations according to some restraints.
> Basically, I want to study all possible conformation of the link between 
> the two domains (8 residues) and freeze the two domains (not completely 
> because I would like to follow the shift of the domains with the 
> conformation change of the link).
> the main goal is to monitor the distance between two residues (located in 
> two different domain) when the conformation of the link is changing.
> In such a case, I can't use dyndom because I've only one pdb file. I tried 
> to define an index file to specify a frozen group of atoms (typically the 
> link is free and the two domains are frozen) but I want the two domains to 
> move with reorientation of the link (like two balls attached by a rope).
> I'm sure this is possible to do in gromacs but I'm not comfortable enough 
> with this program to find the right way to do so immediately.
> has anybody experienced such a problem?  Any help is welcome
This is not trivial. You probably realize you cannot study *all*
conformations... You could probably generate some from the original pdb
file using pymol by rotating a few torsions, then do short simulations
and throw everything together in an essential dynamics analysis...
Most important is that you ask yourself the question what you want to
get out of it....

> thanks
> olivier
> **************************************************
> Olivier WALKER
> Department of Chemistry & Biochemistry
> University of Maryland
> College Park, MD 20742
> **************************************************
> Fax : 301-314-0386
> Phone : 301-405-8710
> E-mail : oliwalk at wam.umd.edu
> **************************************************
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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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