VMD-L Mailing List

From: Ekta Khurana (ekta_at_vitae.cmm.upenn.edu)
Date: Mon Apr 16 2007 - 14:34:47 CDT

  Hi Peter, I get the xyz files from a code developed in the group. As they
are big, I have attached a small xyz file generated using vmd which gives
the same error on using catdcd.
Thanks,
Ekta

On Fri, 13 Apr 2007, Peter Freddolino wrote:

> Could you post the xyz file you're having trouble with? Where did you
> get it from?
> Peter
>
> Ekta Khurana wrote:
>>
>> Hi, I am trying to convert xyz file to dcd file using catdcd using
>> the command "./catdcd -o try.dcd -xyz try.xyz" but I get this message:
>> .........................................
>> CatDCD 4.0
>> Opening file 'try.dcd' for writing.
>> Opened file 'try.xyz' for reading.
>> xyz timestep) missing type or coordinate(s) in file 'try.xyz' for atom
>> '1407'
>> Read 0 frames from file try.xyz, wrote 0.
>> Total frames: 0
>> Frames written: 0
>> CatDCD exited normally.
>> ......................................
>>
>> I have 1408 atoms. I can convert the xyz to dcd using vmd interface
>> but not using catdcd. If I generate xyz file back from dcd using
>> vmd(save coordinates) and try to convert it back to dcd using catdcd,
>> I get the same message. So seems like it's a problem with catdcd
>> plugin. As I wnat to use catdcd for the conversion, any help would be
>> appreciated.
>>
>> Thanks,
>> Ekta
>>
>>
>>
>> ............................
>> Ekta Khurana
>> Center for Molecular Modeling
>> Department of Chemistry
>> University of Pennsylvania
>> Phone: (215) 573-8697
>> Fax: (215) 573-6233
>

  • chemical/x-xyz attachment: try.xyz