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 > > valadie@urbb.jussieu.fr