Re: Trajectory file formats & structural alignment

From: Giovanni Bellesia (gbellesia_at_chem.ucsb.edu)
Date: Thu May 08 2008 - 18:00:18 CDT

Hi,

1) catdcd 4.0
http://www.ks.uiuc.edu/Development/MDTools/catdcd/

2) RMSD Trajectory Tool within VMD
http://www.ks.uiuc.edu/Research/vmd/plugins/rmsdtt/

BTW, both VMD and NAMD web pages contain a lot of information plus an
extended set of links
to documentation files and tutorials. Taking some time to go through
them can be quite helpful !

Giovanni
> Dear VMD users,
>
> I have two question about manipulating trajectory file:
>
> 1) Is there any tool that can be used to convert DCD file to AMBER or
> Gromacs trajectory file format?
>
> 2) How can I align the solute of my system in all my snapshots to that
> of the first frame, and then output them into a new dcd file?
>
> Best,
> Wei
>

-- 
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Giovanni Bellesia
Department of Chemistry and Biochemistry
University of California, Santa Barbara
Santa Barbara, California 93106-9510, USA.
Email: gbellesia_at_chem.ucsb.edu
Phone: 805 893 2767
Web: http://www.chem.ucsb.edu/~sheagroup/
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