VMD-L Mailing List

From: Nicolas Sapay (n.sapay_at_ibcp.fr)
Date: Tue Sep 27 2005 - 10:03:18 CDT

Michel,
What is exactly the problem? Personally, I run ptraj with this type of
command line:
ptraj <foo.psf> <foo.ptraj>
with foo.psf, my structure file and foo.ptraj my ptraj script.
The ptraj script could be something like that

trajin /home/jdoe/namd_projects/production/foo.dcd
strip :TIP3
center :1-28 mass
atomicfluct out /home/jdoe/namd_projects/analysis/foo_rms.txt @CA,C,N
byres
go

This will give you the atomic fluctuation for backbone heavy atoms by
residue in a text file

Nicolas

Le mar 27/09/2005 à 13:24, Michel Espinoza-Fonseca a écrit :
> Hi all,
>
> I would like to know if any of you have tried to analyze NAMD
> trajectories using ptraj. I just tried to do it, but ptraj does not
> work.
>
> Do you have any suggestions?
> Michel
> 

-- 
_ Nicolas Sapay ____________________________________________
  Ph.D sudent in structural bioinformatics
  Institut de Biologie et Chimie des Proteines
  CNRS - Claude Bernard University, IFR128 Bioscience Lyon-Gerland
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  69367-F Lyon cedex 07      Fax: +33 (0)4 72 72 26 04
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