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.
Best regards
-Roja
On Thu, 24 May 2018, 09:55 FyD, <fyd.q4md-forcefieldtools.org> 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
> ---
> http://q4md-forcefieldtools.org/FyD/
>
>
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Received on Wed May 23 2018 - 23:00:02 PDT
