Hi Nida,
Here is the metal ion modeling tutorial for AMBER:
http://ambermd.org/tutorials/advanced/tutorial20/ <
http://ambermd.org/tutorials/advanced/tutorial20/>
We have developed nonbonded model parameters for Hg2+ ion and added them into AMBER program package.
If you want to use the nonbonded model to model Hg2+ ion, you can check the Amber manual page 45 to 47 to get some information about the parameter files.
If you want to use the bonded model to model Hg2+ ion, you can use the MCPB.py program to do the parameterization. Here is a tutorial about it: http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm <http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm>.
Hope it helps,
Pengfei
> On Feb 15, 2016, at 11:43 AM, nida baig <baignida05.yahoo.com> wrote:
>
> Dr Nida Baig
>
> Flat 9, Block A, Opecks Close,
> Slough, Berks.
> SL2 4GE.
>
> Tel: 01753533460
> Mob:07845667159
> Email:baignida05.yahoo.com
>
> On Monday, February 15, 2016 10:24 AM, nida baig <baignida05.yahoo.com> wrote:
>
>
> Dear All,
> I want to simulate a system with mercury (Hg) ions but i don't have mercury parameter files. Can anyone help me and provide me with the files. I will be grateful. Dr Nida Baig
>
>
>
>
>
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Received on Mon Feb 15 2016 - 13:00:05 PST
