VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed May 24 2006 - 16:19:15 CDT

Ioana,
  I just found a tiny bug in the XYZ plugin which causes the behavior
you're seeing. VMD and CatDCD use the plugins in a very slightly different
way, and the XYZ plugin hadn't been fully exercised in the way
that CatDCD does things. I just compiled a new version. Which
platform are you running it on? I can post a new binary for you...

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, May 24, 2006 at 02:11:22PM -0700, Ioana Cozmuta wrote:
> Hi John,
>
> It goes through the all the files and for each it says
> Opened file '1.xy' for reading
> Read 0 frames from file 1.xyz, wrote 0
>
> etc.
> The final trajectory file is empty
> All the files contain the same number of atoms in the same order and if
> I load each individual file into VMD it shows just fine.
>
> I don't have a similar set of pdb files at hand to try with catdcd for
> the same purpose.
>
> Best,
> Ioana
>
>
> John Stone wrote:
> >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/
> >>
> >
> >
>
> --
> 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