Re: [AMBER] Problems in forcefield parameterization of Mercury

From: Muthukumaran Rajagopalan <kumaran.bicpu.edu.in>
Date: Wed, 17 Apr 2019 11:06:14 +0530

Dear Pengfei,

Thank you for the suggestions.

I have mercury chloride connected via co-ordinate bond to chemical compound. Your suggestions will be helpful.

On 04/17/19 07:03 AM, Pengfei Li <ambermailpengfei.gmail.com> wrote:
>
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
-- 
with regards 
R. Muthukumaran
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Apr 16 2019 - 23:00:02 PDT
Custom Search