[gmx-users] MD continuation

Ruben M Buey ruben at akilonia.cib.csic.es
Thu Oct 7 10:34:17 CEST 2004

Hi all,
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.
Can I do a MD simulation starting from the GTP state, take the 
equilibrated structure of this GTP-MD and then remove the gamma phospate 
of this structure and run a new MD with this GDP-bound protein?
Would it be better to compare the two states (GTP and GDP)?
Thanks in advance for your kind attention,

Ruben M Buey. PhD student. Lab 308
Centro de Investigaciones Biologicas
Consejo Superior de Investigaciones Cientificas
Dpt. Protein Function and Structure
C/ Ramiro de Maeztu, 9 
28040  Madrid   (SPAIN)
Phone:   34-918373112 ext 4380
Fax:     34-915360432

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