[AMBER] RMSD for two different MDs

From: Haining Liu <Haining.Liu.175.nd.edu>
Date: Mon, 28 Nov 2016 15:49:02 -0500

Hi Amber list,

I want to compare the RMSD of two different ligands in the same protein to
find out whether they have similar binding. Specifically, I have

protein + ligand 1 (50 ns MD)
protein + ligand 2 (50 ns MD)

ligand 1 and ligand 2 structurally different, but similar. I want to get
the RMSD of ligand 1 and ligand 2 in each of the 50 ns snapshot. Is there a
way to do this by cpptraj?

Thank you very much for your help.

AMBER mailing list
Received on Mon Nov 28 2016 - 13:00:03 PST
Custom Search