[gmx-users] MD continuation

Xavier Periole x.periole at chem.rug.nl
Fri Oct 8 12:15:21 CEST 2004

Ruben M Buey wrote:

> Does it make sense to simulate the GDP-bound state of a protein 
> starting from the equilibrated structure of a MD simulaton of the 
> GTP-bound state.
> I mean, I have the structure of the GTP form but I do not have the 
> GDP-bound structure. 

It makes sense of course but the result is unknown. If you do not have 
any control on the
final structure of the GDP simulation (or mutant simulation) you will 
face the problem of
what is relevant in the changes (if any) happening during the GDP 

One thing you can do is collect as much as possible information 
conserning the GDP form
of your protein and compare your simulation to this data.

Marco Ceruso and myself did some nice work on GDP/GTP conformations 
changes in
transducin. Check the paper :
"Molecular dynamics simulations of transducin: interdomain and front to 
communication in activation and nucleotide exchange."
J Mol Biol. 2004 Apr 30;338(3):469-81.

Hope it'll help.


   Xavier Periole - Ph.D.

   Dept. of Biophysical Chemistry / MD Group 
   Univ. of Groningen
   Nijenborgh 4
   9747 AG Groningen
   The Netherlands

   Tel: +31-503634329
   Fax: +31-503634800
   email: x.periole at chem.rug.nl
   web-page: http://md.chem.rug.nl/~periole

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