VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Apr 20 2007 - 15:36:36 CDT

Hi,
  I've just posted updated catdcd binaries based on the VMD 1.8.6
builds of CatDCD:
  http://www.ks.uiuc.edu/Development/MDTools/catdcd/

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Apr 17, 2007 at 12:48:12PM -0500, John Stone wrote:
>
> Ekta,
> Now that the new VMD release is posted, I'll be updating the CatDCD
> binaries etc as well. We had a busy week last week so some of these
> things are still in-progress.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Mon, Apr 16, 2007 at 10:31:42PM -0400, Ekta Khurana wrote:
> >
> > Thanks Axel. The problem was I was using the pre-compiled binary for
> > catdcd 4.0 from
> > the website, which is not the updated version. May be this binary can be
> > removed from the website or a note added to avoid confusion.
> >
> > Cheers,
> > Ekta
> >
> > On Mon, 16 Apr 2007, Axel Kohlmeyer wrote:
> >
> > >On Mon, 16 Apr 2007, Ekta Khurana wrote:
> > >
> > >
> > >hi ekta,
> > >
> > >please check again. have a look at this:
> > >
> > >[akohlmey_at_athanor ~]$ which catdcd
> > >/usr/bin/catdcd
> > >[akohlmey_at_athanor download]$ catdcd -o tmp.dcd -xyz try.xyz
> > >CatDCD 4.0
> > >Opening file 'tmp.dcd' for writing.
> > >Opened file 'try.xyz' for reading.
> > >Read 21 frames from file try.xyz, wrote 21.
> > >Total frames: 21
> > >Frames written: 21
> > >CatDCD exited normally.
> > >
> > >hmmmm... seems to work ok, right? ;-)
> > >
> > >cheers,
> > > axel.
> > >
> > >EK> Hi Peter, I get the xyz files from a code developed in the group. As
> > >they
> > >EK> are big, I have attached a small xyz file generated using vmd which
> > >gives
> > >EK> the same error on using catdcd.
> > >EK> Thanks,
> > >EK> Ekta
> > >EK>
> > >EK>
> > >EK> On Fri, 13 Apr 2007, Peter Freddolino wrote:
> > >EK>
> > >EK> > Could you post the xyz file you're having trouble with? Where did you
> > >EK> > get it from?
> > >EK> > Peter
> > >EK> >
> > >EK> > Ekta Khurana wrote:
> > >EK> >>
> > >EK> >> Hi, I am trying to convert xyz file to dcd file using catdcd using
> > >EK> >> the command "./catdcd -o try.dcd -xyz try.xyz" but I get this
> > >message:
> > >EK> >> .........................................
> > >EK> >> CatDCD 4.0
> > >EK> >> Opening file 'try.dcd' for writing.
> > >EK> >> Opened file 'try.xyz' for reading.
> > >EK> >> xyz timestep) missing type or coordinate(s) in file 'try.xyz' for
> > >atom
> > >EK> >> '1407'
> > >EK> >> Read 0 frames from file try.xyz, wrote 0.
> > >EK> >> Total frames: 0
> > >EK> >> Frames written: 0
> > >EK> >> CatDCD exited normally.
> > >EK> >> ......................................
> > >EK> >>
> > >EK> >> I have 1408 atoms. I can convert the xyz to dcd using vmd
> > >interface
> > >EK> >> but not using catdcd. If I generate xyz file back from dcd using
> > >EK> >> vmd(save coordinates) and try to convert it back to dcd using
> > >catdcd,
> > >EK> >> I get the same message. So seems like it's a problem with catdcd
> > >EK> >> plugin. As I wnat to use catdcd for the conversion, any help would
> > >be
> > >EK> >> appreciated.
> > >EK> >>
> > >EK> >> Thanks,
> > >EK> >> Ekta
> > >EK> >>
> > >EK> >>
> > >EK> >>
> > >EK> >> ............................
> > >EK> >> Ekta Khurana
> > >EK> >> Center for Molecular Modeling
> > >EK> >> Department of Chemistry
> > >EK> >> University of Pennsylvania
> > >EK> >> Phone: (215) 573-8697
> > >EK> >> Fax: (215) 573-6233
> > >EK> >
> > >
> > >--
> > >=======================================================================
> > >Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> > > Center for Molecular Modeling -- University of Pennsylvania
> > >Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> > >tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> > >=======================================================================
> > >If you make something idiot-proof, the universe creates a better idiot.
> > >
>
> --
> 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 

-- 
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