From: Thakur, Abhishek <axt651.miami.edu>
Date: Mon, 28 Nov 2016 21:27:53 +0000
You can use cpptraj to do RMSD by following the script
Make a trajin file
trajin X.crd.gz
strip :WAT
strip :Ions
rms first out X_RMSD.out time 0.005 :residue range
cpptraj X.prmtop < X.trajin > Y.out
with regards,
AT
________________________________
From: Haining Liu <Haining.Liu.175.nd.edu>
Sent: Monday, November 28, 2016 9:49:02 AM
To: AMBER Mailing List
Subject: [AMBER] RMSD for two different MDs
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?
