Dear Amber users,
I have a protein which has Zn atom, bound directly to four amino acids (Tankyrase PARP domain, 2rf5 code in PDB bank).
I need to test the results of docking of small ligands by MD run by evaluation of the stability of complexes. The binding site is far from Zn atom. For now I have no time to make parametrization for Zn atom as far as it seems to be rather advanced and time consuming. What options do I have?
For example I haven't included Zinc in docking site while performing docking. Can I maybe make CAP molecular dynamics only for the binding site of the ligand.
Probably parametrize zinc as ion, or just cut out Zn atom and fix all Zn-surrounding amino acids as in the X-ray structure?
Best regards,
Andrew
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Received on Wed Jan 13 2010 - 02:30:04 PST
