VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Sep 16 2009 - 23:02:35 CDT

Jim,
  Can you check the permissions on the files $env(VMDDIR)/.vmdrc
and all the startup scripts in $env(VMDDIR)/scripts/vmd/

I'm puzzled why the "ls -al" you did below did not list the
file permissions? Do you have "ls" aliased in your shell?
When I do it, I see the file permissions...

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Sep 16, 2009 at 10:53:24PM -0500, Jim Parker wrote:
> John,
> Thanks for the prompt reply. In answer to your questions
> I cut and paste directly from the console to here...
>
>
> vmd > package require solvate
> 1.3
>
> vmd > ls -al [file join $env(VMDDIR) plugins noarch tcl ]
> /home/surfer/lib/vmd/plugins/noarch/tcl:
> ./ ../ apbsrun1.3/
> atomedit1.0/ autoimd1.6/ autoionize1.2/
> bignum1.0/ biocore1.1/ blast1.1/
> cgtools1.0/ cliptool1.0/ clonerep1.1/
> colorscalebar1.2/ contactmap1.1/ dataimport1.0/
> demomaster1.0/ dipwatch1.2/ dowser1.0/
> exectool1.2/ extendedpdb1.0/ gofrgui1.1/
> hbonds1.1/ idatm0.1/ ilstools1.2/
> imdmenu1.0/ inorganicbuilder0.1/ irspecgui1.1/
> membrane1.0/ mergestructs1.0/ molefacture1.1/
> moltoptools0.1/ multimolanim1.0/ multiplot1.4/
> multiseq2.1/ multiseqdialog1.1/ multitext1.0/
> namdenergy1.2/ namdgui1.2/ namdplot1.0/
> namdserver1.1/ nanotube1.0/ navfly1.0/
> navigate1.0/ optimization1.0/ palettetool1.0/
> paratool1.4/ pbctools2.5/ pdbtool1.0/
> phylotree1.1/ psipred1.1/ qmtool1.1/
> ramaplot1.1/ readcharmmpar1.1/ readcharmmtop1.0/
> resptool1.1/ rmsd1.0/ rmsdtt2.0/
> rnaview1.0/ ruler1.0/ runante0.1/
> saltbr1.0/ seqdata1.1/ seqedit1.1/
> solvate1.3/ ssrestraints1.0/ stingtool1.0/
> symmetrytool1.2/ timeline2.0/ topotools1.0/
> trunctraj1.5/ utilities1.0/ vdna2.0/
> viewmaster2.2/ vmdmovie1.7/ vmdtkcon1.1/
> volmapgui1.1/ zoomseq1.1/
> vmd >
>
>
> Also, in order to begin work on the tutorials I was able to kludge
> together the commands to force VMD to give me a TkConsole by manually
> entering the script listed in plugins/tcl/vmdtkcon1.1/vmdtkcon.tcl. The
> TkConsole appears to work normally once I got it to start.
>
> Cheers,
> --Jim
>
> John Stone wrote:
> >Jim,
> > What happens if you run this command from the VMD text console?:
> >package require solvate
> >
> >And this:
> > ls -al [file join $env(VMDDIR) plugins noarch tcl ]
> >
> >Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >On Wed, Sep 16, 2009 at 09:44:31PM -0500, Jim Parker wrote:
> >
> >>Hello,
> >> I recently installed both VMD and NAMD on an Ubuntu 8.10 32-bit system
> >>from binaries. Both programs work fine separately. However, I would
> >>like to use the VMD GUI extensions menu to interface between VMD and
> >>NAMD, but when I select "Extensions" the menu is blank.
> >>
> >>I found a similar thread on the archives
> >>http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/12227.html
> >>
> >>but the solution provided was to ensure the plugin tree was available to
> >>the user. My plugin tree does exist (as provided by the binary) under
> >>directory <root-vmd-dir>/plugins and <root-vmd-dir>/plugins/noarch/tcl
> >>lists the several directories (or upgrades from them) that are listed on
> >>the archived message.
> >>
> >>I did modify the ./configure script to put my install_bin and
> >>install_library_dir in appropriate positions, and my PATH variable lists
> >>both directories (I wasn't sure if I needed both, but have tried with
> >>and without the install_library_path to no avail)
> >>
> >>The namd2 executable directory is also in the PATH variable.
> >>
> >>Any help would be appreciated,
> >>
> >>--Jim Parker
> >>UTSA Physics and Astronomy
> >>
> >
> > 

-- 
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