VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Wed Oct 02 2013 - 13:24:13 CDT

Hi Huong,

I believe (but haven't tested) that the correct command line is:

catdcd -o test.xyz -otype xyz -stype pdb -s test.pdb test.dcd

The -s flag specifies the structure file (You can't just add it to the
input list). You can also use VMD to do the conversion:

mol new test.psf
mol addfile test.dcd waitfor all
animate write xyz test.xyz waitfor all

-Josh

On 10/02/2013 12:21 PM, 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.