Enerygy Minimization of a homology modelled structure in NAMD

From: Arijit Ghosh (arijit.ghosh_at_niser.ac.in)
Date: Tue Mar 31 2015 - 22:46:49 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.

*Arijit Ghosh*
*4th Year Integrated MSc.*
*School of Biological Sciences*
*National Institute of Science Education and Research*
*Bhubaneswar, Orissa-751005, India*
*Alternate electronic contact: arijitghosh2009_at_gmail.com
*Handheld: +91-986-171-9393*

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