[AMBER] verification of ligand rmsd script.

From: Saman Yousuf ali <saman.yousufali64.yahoo.com>
Date: Wed, 11 Jan 2017 11:11:53 +0000 (UTC)

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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Received on Wed Jan 11 2017 - 03:30:02 PST
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