VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Aug 19 2010 - 20:32:23 CDT

Irene,
  Most likely I need to recompile CatDCD with the latest versions of
the DESRES plugins for Maestro and Desmond. I'll check the versions
and if necessary I'll recompile a new version and send you a note
when it is posted, otherwise I'll let you know and we'll look into
what else might be going on there.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Aug 19, 2010 at 11:19:10AM -1000, Irene Newhouse wrote:
> I just downloaded the latest version of standalone catdcd. I don't want to
> use the VMD plugin because I don't have enough memory for the whole
> trajectory. I want to extract the C-alphas from chain A only & created an
> index file for it.
>
> I entered:
>
> ~/catdcd -o HGbIAcAca10th.dcd -otype dcd -i HGbIAcAca.idx -stype pdb -s
> v4fe3ac-all.pdb -dtr clickme.dtr
>
> I put the .idx file .pdb files in the same dir as clickme.dtr. The pdb
> file contains the entire structure, not just chain A C-alphas.
>
>
>
> I get this message:
>
> CatDCD 4.0
> Reading indices from file 'HGbIAcAca.idx'
> Opening file 'HGbIAcAca10th.dcd' for writing.
> Could not find timekeys file at /timekeys
> Error: could not open file 'clickme.dtr' for reading.
>
> I *do* have a timekeys file, but it's in the same dir as clickme.dtr, not
> in its own dir. It's also called timekeys... So I just tried creating a
> timekeys dir & moved timekeys into it. Still got the same message. Where
> should /timekeys be so this will work? [Yes, it's a bandaid, but I'm all
> for what works fastest].
>
>
>
> Thanks!
>
> Irene Newhouse 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078