From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Wed Apr 01 2015 - 02:07:59 CDT
NAMD might not be the right tool for your current problem. You'll get that
done faster using an integrated tool like UCSF Chimera or pymol that do
minimization and have front-ends for docking software.
On 1 April 2015 at 05:46, Arijit Ghosh <arijit.ghosh_at_niser.ac.in> wrote:
> 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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