Dear amber users,
I am working with protein-ligand interaction and using Amber 11 for
simulation. The protein shows high degree of side-chain conformational
changes and minimal backbone conformational changes during ligand binding.
In order to capture these side chain flexibility, as a initial step, I
would like to do clustering based on the side-chain flexibility (i.e.
categorise different areas in protein based on the degree of side chain
flexibility). Is there a way to do such a calculation in Amber?. Can any
one suggested me a way to proceed with this sort of analysis?
Waiting for your valuable reply.
Thanks in advance
Best regards
Anu
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Received on Mon Apr 01 2013 - 01:00:02 PDT
