Hi Diwan,
The force field parameters for Si will present in the next version of gaff.
But not now. You may derive those parameters yourself following the basic
procedure described in the gaff paper.
Best
Junmei
On Wed, Aug 20, 2008 at 11:15 AM, Abdul Hameed, MohamedDiwanMo <
mabdu3.email.uky.edu> wrote:
> Dear Amber Users,
>
> I am interested in doing MD for a small molecule ligand with silicon atom.
> I am studying the binding mode of the small molecule with the protein active
> site. Unfortunately, I could not find the parameters for silicon.
>
>
>
> I searched the archive and noticed that many other people inquired the same
> but got no answers. And the other alternative suggested by Scott is to use
> the c3 gaff values (as a last resort). It will be very helpful if someone
> can help me regarding the parameters for Silicon related bonds, angles and
> dihedral angles. If you can point to any references, suggestions, links or
> publications it will be very useful.
>
>
>
> Thanks in advance.
>
> Regards,
>
> Diwan
>
>
>
>
>
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Received on Sun Aug 24 2008 - 06:08:05 PDT
