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 <[EMAIL PROTECTED]>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. > >
