[gmx-users] S-S bond

[rose rahmani]

Hi,

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 .itp 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?

Best regards