Ok. Thank you and thank Ross Walker for previous reply.
Zn atom is definitely is not in the binding site. Probably it can influence geometry of whole protein in inappropriate way if I parametrize it as ion, not bound. But I ll try to simulate the binding of known inhibitors to check if there are some crucial changes in protein geometry.
PS the parametrization of Zn bound to amino acids is an interesting task, probably I ll try to do it in future, but it requires pretty much time, and what I need to do now is just check the probability of ligand to bind the binding site by MD\MM-PBSA.
Best regards,
Andrew
13.01.10, 10:20, "Bill Ross" <ross.cgl.ucsf.edu>:
> > Set the charge to +2, the name and type to ZN.
>
> > Create an frcmod file with the contents:
> >
> > Zinc 2+ Params
> > MASS
> > Zn 65.38
> > ...
> > NONB
> > Zn 1.85 0.06
>
> You need to be consistent with the atom name and type name. The type
> name is in the frcmod above, in this case it's Zn so if you use this frcmod
> use Zn as the type name when editing in leap. Whatever you choose for
> the atom name when editing in leap, make sure that's what is in your
> pdb file.
>
> Bill
>
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Received on Thu Jan 14 2010 - 01:30:02 PST
