VMD-L Mailing List

From: Irene Newhouse (einew_at_hotmail.com)
Date: Thu Aug 19 2010 - 22:26:26 CDT

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