Re: [AMBER] RMSD for two different MDs

From: Thakur, Abhishek <>
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,


From: Haining Liu <>
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?

Thank you very much for your help.

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Received on Mon Nov 28 2016 - 14:00:02 PST
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