Hi,

If I understood what you said, you cant assume the ligand conformation of your template as the conformation that this ligand will have in the active site of your model. Some residues might change in your modelled structure, so you ligand will have a different conformation.

I advise you to use a program to dock this ligand into the modelled active site. There is some like: Gold, FlexX and some that are free to use: DOCK, AutoDock.

Ricardo.

On 6/9/06, Frederico Arnoldi fredgca@hotmail.com wrote: > > Dear Modeller's users, > > Could I superimpose the template and the best model of this template and > use > the template's ligand as model's ligand? Which are the theorical problem > of > doing it if I used Modeller to build the model? How precise is it? > > Thanks for the help. > > Fred > UNESP - Brazil > > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > http://salilab.org/mailman/listinfo/modeller_usage >