VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Oct 02 2013 - 12:48:06 CDT

You need to give catdcd a PDB or PSF or something similar that contains
the atom names, otherwise it doesn't know what the name/type of
each atom is, and it can't fill out the first field of the XYZ
file. The DCD file contains no atom names, only coordinates, that's why
you need to give catdcd another file containing structure info...

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Oct 02, 2013 at 01:21:04PM -0400, Huong Vu wrote:
> Hi,
> I am trying to use Catdcd to convert a dcd file to xyz.
> catdcd -o test.xyz -otype xyz test.dcd
> However I got this:
> CatDCD 4.0
> Cannot write timesteps in 'xyz' format without structure file.
> After trying to add pdb file or psf file to the inputfiles, I still get
> the same result. Does that means that I can not convert dcd file to xyz by
> Catdcd?
> Any help is highly appreciated.
> Thanks,
> Huong. 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/