Hi, Sophia,
If you have a structure with many bad contacts, minimizing them with
positional restraints might help to lower the deviation. This can be
done in several consecutive steps in which the restraints are
gradually released. The unrestrained minimization is performed as
the last step. This usually works well. Good luck!
Guanglei
On Tue, 3 Sep 2002, m.elizabeth sophia wrote:
> We are doing some docking studies. Is there a common method for
> minimizing the
> protein structures. In my case the structures of proteins after
> minimization,
> seem to deviate from the original structure. Please assist.
> Sophia
>
>
--
Guanglei Cui
Dept. of Chemistry
SUNY at Stony Brook
Stony Brook, NY 11790
Received on Tue Sep 03 2002 - 06:19:39 PDT
