VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Aug 24 2010 - 16:44:25 CDT
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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
- Next message: John Stone: "Re: runsqm plugin required but not installed"
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- In reply to: Irene Newhouse: "RE: catdcd usage with Desmond trajectory"
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