VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Mon Apr 16 2007 - 19:51:35 CDT

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.