Re: [AMBER] verification of ligand rmsd script.

From: Elvis Martis <>
Date: Wed, 11 Jan 2017 14:38:15 +0000

It looks fine to me.
Just check if all your ligand atoms match the atom_masks you have mentioned and the prmtop file name is correct.

    Best Regards

Elvis Martis
Ph.D. Student (Computational Chemistry)
 at Bombay College of Pharmacy

A  Kalina, Santacruz [E], Mumbai 400098, INDIA
Skype. adrian_elvis12

-----Original Message-----
From: Saman Yousuf ali []
Sent: Wednesday, January 11, 2017 4:42 PM
To: AMBER Mailing List <>
Subject: [AMBER] verification of ligand rmsd script.

Dear All,I need a cpptraj script to calculate rmsd of ligand throughout md. I searched some tutorial in which following script for  used for plotting ligand rmsd; parm file.prmtop trajin reimaged.mdcrd rms first :297.C*,N*,O*,S*,F*,Cl* out rmsd.datstrip :WAT strip :Na+ Is it fine for calculating small molecule rmsd?

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