Re: [AMBER] S-S bond

From: FyD <>
Date: Fri, 01 Jun 2018 07:22:31 +0200

Dear Roja,

> Thank you so much francois, but would you please give an straight solution
> or tutorial? I have not worked with this software and i'm really in hurry.

I missed your email :-)

For the use of intra-mcc see for instance:
(however the application presented is different to yours).

That being written I am not sure you will be able to successful
generate 'in hurry' a force field for your nanotube molecular fragment.

regards, Francois

> On Thu, 24 May 2018, 09:55 FyD, <> wrote:
>> Hi,
>> 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 Thu May 31 2018 - 22:30:02 PDT
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