Enerygy Minimization of a homology modelled structure in NAMD

From: Arijit Ghosh (arijit.ghosh_at_niser.ac.in)
Date: Sun Mar 29 2015 - 21:16:03 CDT


Can someone please let me know if I can energy minimize a homology modelled structure in NAMD? I mean to ask if it's possible in NAMD to relax the sidechains so there are minimum sidechain clashes after the minimization. I have one model and three mutated models.

Again, after docking a ligand, can the same be done and find the best binding affinity (in terms of binding energy)?


P.S.: I'm really novice.

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