On Sat, Apr 28, 2012 at 9:05 AM, Navin Jain <njain.amber.gmail.com> wrote:
> Hi everyone,
> I would like to study the interactions of silver atoms (zero charge)
> with a protein molecule. However, I am facing difficulty in preparing
> silver parameter file. In addition, can anyone suggest the best force
> field to study metal protein interactions.
>
A neutral silver atom? That seems unusual. With no charge, the silver
atom will just act like an ideal gas (i.e., it will only have dispersive
van der Waals terms). I am skeptical that you would learn anything from a
force field description of this system (it's also very unusual to have
silver -not- in an ionized form in solution...). I am convinced you would
not learn anything interesting from a fixed-charge force field, and even
using a polarizable force field is still unlikely to yield insight.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Apr 28 2012 - 10:00:03 PDT
