VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Aug 26 2003 - 13:32:18 CDT

Raymond,
  The problem you're having on Linux is because you're running VMD 1.6!!!
In order to use psfgen, solvate, or any of the plugins written in the
last several years you need to install VMD 1.8.x on your machine.
The version you're using now is 2 years old, which may not seem like
much, but from the point of view of VMD development, that's ancient
history already! :)

If you need help getting the new version installed on Linux, let me know.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Aug 26, 2003 at 02:38:08PM -0400, Raymond C. Fort Jr. wrote:
> At 01:04 PM 8/26/03 -0500, you wrote:
>
> >Raymond,
> >
> >On Tue, Aug 26, 2003 at 01:54:48PM -0400, Raymond C. Fort Jr. wrote:
> >> Thanks for your patience with my fumbling. I have no problem executing
> >the
> >> package require command under Windows, and the solvate script works
> >with no
> >> problems.
> >
> >Good, that's how it is supposed to work... :)
> >
> >> However, on a Linux box, the "package require" command brings the
> >response
> >> "cannot find package solvate". Likewise the "package require psfgen"
> >> command.
> >
> >That's very interesting. Can you email me the messages that
> >VMD prints out when it starts up, and then a transcript of the output
> >you get when you run 'package require xxxx' so I can see the exact
> >error you're getting? What version of Linux are you running by the way?
>
> Info) vmd for LINUX, version 1.6.1a2 (March 5, 2001)
> Info) VMD WWW Page: http://www.ks.uiuc.edu/Research/vmd/
> Info) Please email all comments and bug reports to vmd_at_ks.uiuc.edu
> Info) The authors request that any published work which utilizes
> Info) VMD please include the following reference:
> Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> Info) -------------------------------------------------------------
> Info) Multithreading available, 2 CPUs detected.
> Info) Stereo in a window is NOT available.
> No default configuration 'mesa3.1' in init file
> Info) Opened sensor config file /usr/local/VMD/lib/.vmdsensors
> vmd > package require solvate
> can't find package solvate
> vmd >
>
> This particular box is RedHat 6.2; I also have the same problems on 7.2; I
> know, these are old, but I tend to get a stable system and then not upgrade
> until forced to do so.
>
>
> >> It makes no difference whether the two files are in directories
> >> in my path, or in the same directory with VMD. The pkgIndex.tcl file
> >is in
> >> the directory with solvate.
> >
> >Where do you have VMD itself installed? /usr/local/lib/vmd?
>
> /usr/local/VMD
>
> >> I'm suspecting that some environment variable is not properly set. but
> >> would certainly appreciate any other suggestions you may have.
> >
> >It could be that there's something messed up with your Linux installation,
> >if you email me the /usr/local/bin/vmd startup script and a directory
> >listing
> >or two, I should be able to determine what is going wrong with your Linux
> >box.
>
> The vmd startup is attached; following are the listings of /usr/local/VMD
> and /usr/local/VMD/lib. The full installation of NAMD, including psfgen,
> is in /usr/local/NAMD.
>
> >No problem, I know VMD can be complicated to use at times, and people often
> >find little bugs I've never seen before, so I'm happy to help when people
> >run into these sorts of things. Yours is the first time I've heard of
> >problems
> >with the 'package require' command. The 'package require' command is
> >so fundamental that I'm concerned that if that isn't working then there's
> >something seriously wrong with your VMD install on Linux, so I want to
> >make sure that we figure out why you're getting that error as it may help
> >prevent a great many problems down the road.
>
> I'm sure the problem is that I've done something stupid, like screwing up
> the way I installed VMD, which works just fine, except for this problem
> with scripts. Of course, the easy way to deal with a stupid mistake is to
> have someone look over your shoulder and see the solution straightaway.
>
> Thanks for your help!
>
> Ray
>
>
>
> >Thanks,
> > John Stone
> > vmd_at_ks.uiuc.edu
>
> Professor Ray Fort Jr. Voice: (207)-581-1180
> Department of Chemistry FAX: (207)-581-1191
> University of Maine EMail: rcfort_at_maine.edu
> Orono, ME 04469 Web:
> chemistry.umeche.maine.edu/fort.html
>
> Molecular modeling of organic and biological molecules; wood and pulping
> chemistry
> 

-- 
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