VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Feb 01 2010 - 21:10:15 CST

On Mon, 2010-02-01 at 20:25 -0600, martin klvana wrote:
> Hello,

martin,

> I use VMD 1.8.7 (Windows 7 / 64bit). I can do the following manually
> (with mouse and keyboard) and by writing corresponding commands, one
> by one, in Tk Console:
> load reference pdb file >>> load dcd trajectory >>> save dcd

before loading the .dcd file, you should delete the coordinates
from the .pdb file or else you will have the the same coordinates
in the first frame. you can also simply load a .pdb file and then
save it (only for the purposes of conversion) as a .psf file.

> trajectory with stride set to some value
>
> It works fine.
>
> However, when I put all the commands into a single file and execute
> Load State (in the Main Menu) or Load File (in the Tk Console), I get
> the following error message:
>
> ERROR: Illegal frames requested for coordinate file I/O

i'd have to see the script file to know for sure.
if you use something like

mol new xxx.psf waitfor all
mol addfile xxx.dcd waitfor all

to read the files, then this should
not be any problem.

> Is it a bug?
>
> (Note: I can run catdcd on remote linux or macx machine, but I would
> like to process my trajectories rather on my windows machine and
> catdcd is not available for Windows as far as I know.)

this is a strange view. wouldn't it be easier to first process
the files where they are created and then transfer only the
result? particularly, if you use a script anyways...

cheers,
   axel.

>
> Thanks for any comment on this issue,
> martin 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com 
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.