VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Oct 02 2013 - 13:13:18 CDT

On Wed, Oct 2, 2013 at 7:21 PM, Huong Vu <vuhuongiop_at_gmail.com> 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?

please read the docs.

if you do it right, it works.

[akohlmey_at_zero catdcd]$ ./catdcd -o test.xyz -otype xyz -s alanin.psf
-stype psf alanin.dcd alanin2.dcd
CatDCD 5.1
Opening file 'test.xyz' for writing.
dcdplugin) detected standard 32-bit DCD file of opposite endianness
dcdplugin) X-PLOR format DCD file (also NAMD 2.0 and earlier)
Opened file 'alanin.dcd' for reading.
Read 100 frames from file alanin.dcd, wrote 100.
dcdplugin) detected standard 32-bit DCD file of native endianness
dcdplugin) X-PLOR format DCD file (also NAMD 2.0 and earlier)
Opened file 'alanin2.dcd' for reading.
Read 100 frames from file alanin2.dcd, wrote 100.
Total frames: 200
Frames written: 200
CatDCD exited normally.

> Any help is highly appreciated.
>
> Thanks,
> Huong. 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.