Thanks! I think we still can't tell if the mutant would disturb ligand binding or not. Best! Hongmin
On Wed, Dec 3, 2008 at 2:15 PM, Juergen Bosch <[EMAIL PROTECTED]>wrote: > 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 <[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. >> >> > > - > 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 > >
