Dear Jagur,
> I am planning to carry out a MD simulation of a protein having a
> Zinc ion with five coordination bonds.
> I would like to ask a question about the parameters for the Zinc.
> Can anyone please let me know, how to prepare the parameters for
> such type of Zinc ion.
> I am using AMBER 11/AmberTools.
1) You could first consider your Zinc atom with a +2 total charge.
Here, (i) either you use the Amber force field topology database for
the amino-acid ligands (you might need to carefully equilibrate the
active site), (ii) or you derive the charges of the active site with
the amino-acid ligands extracted from the protein (here you need to
constraint the charge value of the Zinc atom to a +2 value during the
charge fitting step).
2) or you could consider your Zinc atom with a total charge
delocalized on the amino-acid ligands. Here you derive the charges of
the entire site extracted from the protein [as in approach 1) (ii)]
without constraining the charge value of the Zinc atom during the
charge fitting step.
Personally, I prefer the approach 1) (ii) and 2) as you use a QM
geometry optimization step that allows studying the metal complex by
QM. That being said, these approaches are far more time consuming. If
you decide to use of these approaches you could use R.E.D. Server .
http://q4md-forcefieldtools.org/.
regards, Francois
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Received on Wed May 09 2012 - 05:00:02 PDT
