Re: [AMBER] S-S bond

From: FyD <>
Date: Thu, 24 May 2018 07:24:55 +0200


You could use PyRED to generate your nanotube molecular fragment,
starting from an alkyl disulfide nanotube derivative and using an
intra-molecular charge constraint to remove that alkyl group and one
sulfur atom...

regards, Francois

> I want to functionalize ZnS nanotube with different molecules which all
> have sulfur in their structures, like cystein amino acid and ... . I want
> to study the interaction of this functionalized nanotube with different
> proteins.
> I use DFT for calculating the partial charges and bond length in ZnS
> nanotube and made an topology file for it.
> If i know that cystein (and all those molecules) can BIND to ZnS with their
> sulfur atom, can AMBER define this this S(from cystein)-S(from ZnS
> nanotube) bond? Is this special S-S bond like that S-S which is in amber?
> There is an article which correspond to interaction of ZnS with cystein by
> umbrella sampling. In this article the binding energy and bond length in
> minimum PMF is calculated. How about this bond length? It couldn't be used
> as S-S bond length for ZnS nanotube cystein?
> Is it better to use DFTcalculation for all these structures and just do
> functionalized nanotube with protein by AMBER force field?
> Could you please help me?

           F.-Y. Dupradeau

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Received on Wed May 23 2018 - 22:30:02 PDT
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