Yes, it is better to have MD or energy minimization. Otherwise, with only view on the screen, we can't tell if the mutated residue would disturb ligand binding because of the side chain flexibility.
Best!
Hongmin

On Wed, Dec 3, 2008 at 12:50 PM, Juergen Bosch <[log in to unmask]> wrote:

Pymol
the question is, into how much trouble do you want to get ?
MD simulations ? Energy minimisation ? Then you will need to do more than just mutate on the sreen one residue with Pymol.

Jürgen

On 2 Dec 2008, at 17:29, Hongmin Zhang wrote:

Dear All,
  I am trying to mutate a single amino acid in a PDB to see if the mutant
disturbs ligand binding. Does anyone know any software that can do such work?
Thanks a lot!

-
Jürgen Bosch
University of Washington
Dept. of Biochemistry, K-426
1705 NE Pacific Street
Seattle, WA 98195
Box 357742
Phone:   +1-206-616-4510
FAX:     +1-206-685-7002
Web:     http://faculty.washington.edu/jbosch

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