On Wed, 2014-09-17 at 12:56 +0200, Soumendranath Bhakat wrote:
> Dear Amberists;
>
> We have a branched chain silver salt (attached herewith) on which we want
> to run a molecular dynamics simulation to understand conformational
> arrangement.
>
> But we didn't find any parameters to simulate salt systems. Will it be
> possible to simulate silver salts using AMBER 14.
This is a highly unusual molecule relative to what people typically
study using AMBER. You can try using antechamber to generate the
parameters for the small molecule. I don't see any monovalent silver
ion parameters (only divalent, which is strange to me since +1 is the
more common oxidation state).
You would have to check your parameters against any kinds of
experimental measurements you can find to validate the parameter set.
The parameter sets included with Amber may not help much with the silver
parameters...
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Sep 17 2014 - 05:00:05 PDT
