VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed May 24 2006 - 15:58:23 CDT

Hi Ioana,

Try this and see if it works for your XYZ files. I tried it on one of my
XYZ files here and had a minor problem which I'm looking into, but it works
fine for PDB and other types. It could be that I've got a bug to fix in the
current version of the XYZ plugin. But try this and tell me if it works for
you:
  catdcd -o new.dcd -xyz *.xyz

for PDB:
  catdcd -o new.dcd -pdb *.pdb

Note that the coordinate files will have to have consistent atom counts etc..

  John

On Wed, May 24, 2006 at 01:38:54PM -0700, Ioana Cozmuta wrote:
> Hi John,
>
> Thank you for the link. Say I have a series of xyz files 1 through 1000
> what is the correct syntax and the best way to use catdcd to generate
> the dcd file?
>
> Ioana
>
> John Stone wrote:
> >Try the latest version of CatDCD, which should be able to read the XYZ
> >file and turn it into a DCD for you:
> > http://www.ks.uiuc.edu/Development/MDTools/catdcd/
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >
> >On Tue, May 23, 2006 at 04:55:51PM -0700, Ioana Cozmuta wrote:
> >
> >>Hi vmd users,
> >>
> >>I have a series of .xyz files as snapshots of a trajectory. Is there an
> >>easy and quick way to turn this into a .dcd trajectory file?
> >>
> >>thank you,
> >>Ioana
> >>
> >
> >
>
> --
> Ioana Cozmuta, Ph.D
> Eloret Corporation
> NASA Ames Research Center
> Mail Stop 230-3
> Moffett Field, CA 94035
> phone (650) 604-0993
> e-mail: icozmuta_at_mail.arc.nasa.gov
> http://people.nas.nasa.gov/~ioana/ 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078