VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Mon Apr 16 2007 - 21:31:32 CDT

The latest version (from the vmd 1.8.6 tree) should indeed be working
ok; this was only updated late this afternoon. Ekta, please download
catdcd again and a give it another shot.
Peter

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> >
>
>