Dear Pranjal,
You could adopt two different approaches:
-1 consider Mg2+ to have a +2 total charge; here two possibilities:
-1.1 the most simple one: you use the FF libraries form the FF you
are going to load in LEaP for the ligands of Mg2+ (i.e. the amino
acids, AA) and you define/or use a FF library for Mg2+ (or any MgX2
complex)
-1.2 you re-derive the charge values for the active site and set a
constraint during the charge fitting step so that the charge of Mg2+ =
'2'.(or '0' for any MgX2 complex). Here you have to cap the AAs of the
capping site (or remove the backbone).
-2 consider Mg2+ to have a delocalized charge value on its ligands.
in this case you have to define the topology i.e. the bonds between
the ligands and the Mg atom. Then, you follow the same approach than
in 1.2 but without the constraint.
These approaches can be applied for wild types and variants...
See an example in R.E.DD.B. with a Fe3+ metal center:
http://q4md-forcefieldtools.org/REDDB/projects/F-88/
See R.E.D. Server:
http://q4md-forcefieldtools.org/REDS/
regards, Francois
> 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?
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Received on Fri Jun 21 2013 - 00:30:03 PDT
