dear Helene,
it is not straightforward to generate water molecules around certain parts of
your protein but if water molecules exist in the template structure then it
is easily can be included in the model building and optimization.
(Alternatively you can use some other programs to immerse your template protein
in a solvent environment.) Please look at the WATER_IO command in the manual
(SET WATER_IO= on). Also you might want to change the TOPOLOGY_MODEL = 1, in
order to include all atoms i.e. hydrogens as well (READ_TOPOLOGY FILE =
'$(LIB)/top_allh.lib' and SET TOPOLOGY_MODEL = 1). Note that these waters do
not really play a role of a dynamic solvent because they position will be
restricted by distance and angle restraints derived from the template+water
complex struture.
best wishes
Andras
Helene Valadie wrote:
>
> Hello,
>
> I am student in France and I would like to know if it is possible to
> build a model with adding water
> molecules on a part of my molecule (for example, add water molecules
> only on the Nterm atoms of
> my molecule).
> Thank you,
>
> Helene VALADIE
>
>
--
,
Andras Fiser, PhD # phone: (212) 327 7206
The Rockefeller University # fax: (212) 327 7540
Box 270, 1230 York Avenue # e-mail:
New York, NY 10021-6399, USA # http://salilab.org/~andras