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In that case you might want to use CNS with model_anneal.inp or model_minimize.inp, or the equivalents in phenix Jürgen On 2 Dec 2008, at 21:29, Hongmin Zhang wrote: > 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 > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the sender > and properly > dispose of the e-mail. > > - 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