From owner-nwchem-users  Thu Mar 15 10:38:26 2001
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Date: Thu, 15 Mar 2001 10:34:42 -0800
From: "Windus, Theresa L" <Theresa.Windus@pnl.gov>
Subject: RE: ligand's rmsd
To: "'Letizia Barreca'" <LBarreca@uh.edu>, nwchem-users@emsl.pnl.gov
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Lety,
  I don't know if you ever got a reply to your question, but here is what Tjerk
Straatsma had to say about the problem.

Theresa

The answer to this one is to add to the analysis input:


analysis
 system xxx
 reference xxx_md.rst
 file xxx_md.trj
 select _CA
 rmsd
 scan zzz
end

task analysis


This will analyze the trajectory xxx_md.trj, using only the CA atoms for the
superimposition in the rms deviation calculation.
Results will be written to zzz.rms and can be viewed with the java tools.

> -----Original Message-----
> From: Letizia Barreca [mailto:LBarreca@uh.edu]
> Sent: Wednesday, February 21, 2001 2:33 PM
> To: nwchem-users@emsl.pnl.gov
> Subject: ligand's rmsd
> 
> 
> Hi all,
> I'm a new user of NWChem.
> I've got two nanoseconds dynamics trajectory of  a  ligand/enzyme
> complex .
> I'd like to analyze  the root mean square deviations  from 
> the reference
> structure just for the ligand .The rmsd should be calculated 
> based on a
> superposition of all Calpha atoms..
> 
> Could somebody help me with this?
> 
> Thank you in advance
> 
> Lety
> --
> Maria Letizia Barreca, PhD
> Department of Biology and Biochemistry
> University of Houston, Houston, TX 77204-5513
> Phone: (713) 743-8367
> E-mail: lbarreca@uh.edu
> 
>