VMD-L Mailing List

From: Jim Parker (jim.parker_at_prismsciences.com)
Date: Wed Sep 16 2009 - 22:53:24 CDT

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
>>
>
>