VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Dec 09 2009 - 09:11:33 CST

Miguel,
  The new message is fine, that just tells you that you're picking
up the dynamically loaded plugin in place of the one that was
statically linked into VMD before.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Dec 09, 2009 at 10:19:44AM +0000, Miguel Costa wrote:
> Hello.
>
> Sorry, only today I had a chance to test the plugin on the platform where
> it failed more often. It seems to be working now, and it will be used
> frequently, so if the error pops up again I'll let you know.
>
> I just noticed, though, that I get a message "Found 2 plugins or data
> handlers in the directory" ..../LINUXAMD64/molfile, which didn't appear
> before, but there is only one copy of the file - is that a problem? I had
> replaced the plugin using your first option, in place.
>
> Thanks again.
>
> Cheers,
> Miguel
>
> On Fri, Dec 4, 2009 at 11:28 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> Our friends at D. E. Shaw Research sent me a bug fix this
> afternoon and I've compiled a fresh set of dtrplugin binaries
> containing the fix. I've posted a tar file containing builds of
> dtrplugin for several common platforms on the VMD web page here:
> http://www.ks.uiuc.edu/Research/vmd/alpha/bugfix/dtrplugin.tar.gz
>
> You can either copy the updated dtrplugin binary into your local
> VMD installation or put it in another directory and tell VMD to
> scan the other directory for plugin updates using a .vmdrc addition
> similar to this one:
> set myplugindir [file join $env(HOME) myplugins [vmdinfo arch] molfile]
> *.so
> vmd_plugin_scandirectory $myplugindir
>
> Let me know if you are able to use the updated dtrplugin or not.
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, Dec 04, 2009 at 09:07:32PM +0000, Nuno Sousa Cerqueira wrote:
> > Hello,
> >
> > I am running on mac and linux systems.
> > But the error is giving on the CentOs (linux-64) system.
> > If you could send me the bug fix I would appreciate a lot .
> >
> > Regards,
> >
> > Nuno
> >
> > On Dec 4, 2009, at 7:54 PM, John Stone wrote:
> >
> > >
> > >Hi,
> > > I got a dtrplugin bug fix from our colleagues at D.E. Shaw Research,
> > >and I should be able to make new plugins containing this fix
> available
> > >soon. What platform(s) are you running on?
> > >
> > >Cheers,
> > > John Stone
> > > vmd_at_ks.uiuc.edu
> > >
> > >On Thu, Dec 03, 2009 at 11:43:02PM +0000, Nuno Sousa Cerqueira wrote:
> > >>Hello,
> > >>
> > >>I am still having problems in readinf desmond trajectories using a
> > >>script.
> > >>my code is like this:
> > >>
> > >> # load Maestro File
> > >> puts "\n####### Loading Maestro File ...."
> > >> mol new $lambdaDirectory/$rootFile-in.cms waitfor all
> > >> display update ui ; # update vmd view
> > >>
> > >> #load trajectory dtr
> > >> puts "\n####### Loading Desmond trajectory ....."
> > >> mol addfile [pwd]/$lambdaDirectory/$rootFile\_trj/clickme.dtr
> > >>waitfor all molid top
> > >> display update ui ; # update vmd view
> > >>
> > >>
> > >>is this the best way to load the trajectory?
> > >>Something it complains about a missing file. It seems that there is
> a
> > >>problem in reading the directory scheme where the trajectory files
> > >>are
> > >>stored.
> > >>
> > >>Any idea.
> > >>
> > >>
> > >>Regards, Nuno
> > >
> > >--
> > >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 

-- 
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