[gmx-users] Fwd: clustering based on side-chain conformations

[anu chandra]

Dear amber users,

I am working with protein-ligand interaction. 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 Gromacs?. 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