VMD-L Mailing List

From: Jim Parker (jim.parker_at_prismsciences.com)
Date: Thu Sep 17 2009 - 19:10:07 CDT

John,
  Thanks so much for working with me. I had attempted to install VMD
previously with mixed results, and the second install was the one that
"worked" except for the Extensions menu. I found some references to the
old path, and that lead me to completely removing all traces of VMD from
my libraries and executable directories, re-install and
Viola...everything works.

Now, I have a question on CUDA, but that will be another thread...

Cheers,
--Jim Parker
UTSA Physics and Astronomy

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
>>>
>>
>>
>
>