Re: [AMBER] verification of ligand rmsd script.

From: Daniel Roe <>
Date: Wed, 11 Jan 2017 09:46:41 -0500

First, I *strongly* recommend you read the cpptraj section of the
Amber 16 manual; in particular look up the commands you are using and
make sure you understand what each is doing.

On Wed, Jan 11, 2017 at 6:11 AM, Saman Yousuf ali
<> wrote:
> 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

You specified two masks; if you look at the manual entry for the
'rmsd' command you will see that the first mask selects atoms in your
frames (i.e. the target atoms), while the second mask selects atoms in
your reference structure. So what you've told cpptraj to do here is
calculate the RMSD of all atoms selected by C*, N*, O*, S*, F*, and
Cl* in residue 297 for frames read in from 'reimaged.mdcrd' to all
atoms selected by :WAT (i.e. all water atoms) in the first frame. This
is almost certainly not what you want to do.

> strip :Na+

Unless you will be writing out a trajectory or doing some other kind
of action, this 'strip' command seems pointless to me.

Again, please read the manual to try and understand the commands you
are using. You may also find the following tutorial helpful:


Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
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Received on Wed Jan 11 2017 - 07:00:03 PST
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