> Two Zinc ions was embedded in the protein which i want to simulate with AMBER, the one Zinc ion coordinated with 3 HIS,and the other one coordinated with HIS ,CYS ,ASP and a structure water molecule.
>
> Unfortunately, i didn't find the corresponding parameters could be used in AMBER for these two protein-metal coordination system after i searched through our Mailing List and consulted the related papers. As a beginner for AMBER, i have litter idea for how to get or develop these parameters properly. So could someone be so kindly to give me some helpful guide for this tough problem? Or could someone have the similar experience and have developed these parameters could be used in AMBER ff?
>
> Any suggestions will be greatly appreciated! Thanks everyone in advance!
Since the Zns are coordinated and not bonded, maybe you could use
standard residues, and enforce the coordination with nmr restraints.
This would save effort in parameterizing angles and dihedrals with Zn.
Bill
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Received on Fri Sep 16 2011 - 09:00:03 PDT
