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
W www.elvismartis.in
Skype. adrian_elvis12
-----Original Message-----
From: Saman Yousuf ali [mailto:saman.yousufali64.yahoo.com]
Sent: Wednesday, January 11, 2017 4:42 PM
To: AMBER Mailing List <amber.ambermd.org>
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?
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jan 11 2017 - 07:00:02 PST
