Hi Aashish,
As Dave said, if you are trying to simulate a AuCl solid, MCPB.py was not originally designed for that.
In this case, you can use the CartHess2FC.py program in the AmberTools to estimate the bond and angle
force constants in the AuCl cluster.
The extended Born cycle could be used to determine the partial charges of Au and Cl ions in the AuCl cluster:
Heinz, H.; Suter, U. W. J. Phys. Chem. B 2004, 108, 18341-18352.
Above are just some thoughts may be worth of trying, but they are not guaranteed to work.
Kind regards,
Pengfei
> On Apr 16, 2018, at 8:15 PM, David A Case <david.case.rutgers.edu> wrote:
>
> On Mon, Apr 16, 2018, Aashish Bhatt wrote:
>>
>> I am trying to simulate AuCl complex with protein. I have made Zn++ force
>> field parameter via MCPB.py method But in that case Zn++ was bound to
>> protein.
>> Can I use mcpb.py for AuCl complex also even though it is not bound to any
>> residue.
>
> Are you referring to AuCl as a solid, somehow interacting with a
> protein; is there water around? (Note that AuCl has a tendency to
> disproportionate into metallic Au and AuCl3 when in contact with water.)
>
> For such a situation, MCPB won't help: it is designed for situations
> where cation and anion dissoicate, and the metal cation is bound to
> protein atoms.
>
> ...hope this helps....dac
>
>
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Received on Wed Apr 18 2018 - 14:30:02 PDT
