VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed May 04 2011 - 22:36:41 CDT

Hi,
  The VMD DTR plugin was donated by D. E. Shaw Research, so I don't know
much about how the files are generated by desmond during a run or when
the timekeys component is populated. Are you running VMD 1.9, or an
older version? VMD 1.9 includes the latest version of the DTR plugin.
If updating to VMD 1.9 doesn't affect your results, then I think
the best thing would be to contact the support channel for desmond
users and ask there, as they can probably comment about whether
it should be possible to read an in-progress desmond trajectory or not.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, May 02, 2011 at 11:40:30AM -0400, Davide Provasi wrote:
> Hi -
> I am trying to read a desmond trajectory, with
>
> mol new small-md.cms waitfor all
> mol addfile /work/home/negria01/scratch/negria01/small-md1_trj/clickme.dtr
> first 10000 last 10999 step 5 waitfor all molid top
>
> this works if the simulation is finished, but while the simulation is
> still running, I get:
> vmd > Could not find timekeys file at /timekeys
> ERROR) Could not read file
> /work/home/negria01/scratch/negria01/small-md1.1/small-md1_trj/clickme.dtr
> Unable to load file
> '/work/home/negria01/scratch/negria01/small-md1.1/small-md1_trj/clickme.dtr'
> using file type 'dtr'.
> vmd >
>
> Is there a way to read in vmd a desmond trajectory while it is still being
> produced?
> thanks
>
> Davide 

-- 
NIH Resource 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/       Fax: 217-244-6078