I am very new in Molecular Dynamics Simulation and hence in Amber MD
package.
I have a few basic doubts and really need your suggestions.
I want to start a MD simulation of a protein and its mutant.
(a).The wild type protein has a Mg2+ binding site (have seen in the crystal
structure) *in the C-terminal end* and biochemical studies shown the
importance of Mg2+ in both activity and stability. Also *crystallization
condition* contains MgCl2.
(b) In the mutant (*N-terminal mutation*) structure, Mg2+ was not observed
in the structures although Mg2+ was present in the crystallization
conditions. The mutant is less stable than the wild type protein.
Is it possible to look the by MD simulation , why Mg2+ is not bound in the
mutant structure? Since mutation site is different from the Mg2+ binding
site.
(c) Can I add counter-ions Mg2+ ions together with Na+ ion for charge
neutralization for better mimic of experimental conditions?
with regards,
Pranjal
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jun 20 2013 - 12:00:21 PDT
