Hi Muthukumaran,
You can use MCPB.py to parameterize the metal site: http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm <http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm>.
Hope it helps,
Pengfei
> On Apr 16, 2019, at 1:24 PM, Muthukumaran Rajagopalan <kumaran.bicpu.edu.in> wrote:
>
> Dear AMBER users,
>
> (i) I am trying to generate force field parameters for Mercury chloride connected via co-ordinate bond to amino acid. Antechamber recognises this coordinate bond as non-bonded. The command used is antechamber -i file.mol2 -fi mol2 -o min_sqm.mol2 -fo mol2 -c bcc -j5 -dr no. But parmchk is not able to define the bond and angle parameters correctly. how to rectify it?
>
> (ii) Next, I tried to generate force field parameters by RESP method. The compound was optimised using Gaussian (Mp2; lanl2dz). The force constants are derived from frequency calculations. Can these frequencies used as force constants? Or any other alternatives to proceed?
>
> Any suggestions and pointers regarding this would be very helpful.
>
> Thanks in advance.
>
> Muthukumaran Rajagopalan
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Received on Tue Apr 16 2019 - 19:00:02 PDT
