From: Irene Newhouse (einew_at_hotmail.com)
Date: Wed Aug 25 2010 - 15:33:25 CDT

Thaks so much! I downloaded it & unfortunately, I get exactly the same behavior. I'm using a desmond traj that's had the Desmond equivalent of a catdcd with stride done on it & I think I should really try this on an untreated segment on the machine on which Desmond was run - but that was done by someone else in the group who's working on a proposal with a deadline looming rapidly, so it may have to wait...
 
Thanks again!
Irene
 
> Date: Tue, 24 Aug 2010 16:44:25 -0500
> From: johns_at_ks.uiuc.edu
> To: einew_at_hotmail.com
> CC: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: catdcd usage with Desmond trajectory
>
>
> Irene,
> There was one small bug fix that DESRES sent us in December 2009 for
> the dtrplugin code, that might affect it correctly finding the
> "clickme.dtr" file. If you want to try the new version of the plugin
> with CatDCD, it is included in the test versions of VMD 1.8.8, which
> are posted in the VMD alpha test area on biofs, described here:
> http://www.ks.uiuc.edu/Research/vmd/alpha/
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Thu, Aug 19, 2010 at 05:26:26PM -1000, Irene Newhouse wrote:
> > Thanks! Actually, if you can tell me where timekeys is expected to be,
> > I'll just gerrymander the directory structure to match:-).
> >
> > Irene
> >
> > > Date: Thu, 19 Aug 2010 20:32:23 -0500
> > > From: johns_at_ks.uiuc.edu
> > > To: einew_at_hotmail.com
> > > CC: vmd-l_at_ks.uiuc.edu
> > > Subject: Re: vmd-l: catdcd usage with Desmond trajectory
> > >
> > >
> > > 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
>
> --
> 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