VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Aug 12 2004 - 16:14:01 CDT

Hi Stephen,
  Have you read the VMD compilation instructions here?:
http://www.ks.uiuc.edu/Research/vmd/doxygen/compiling.html#compiling
http://www.ks.uiuc.edu/Research/vmd/plugins/doxygen/compiling.html

The plugins directory is intentionally NOT inside the vmd directory,
as explained in the online Programmer's documentation. You need to do the
"plugin distribution directory" step at the end of that second page above.

Normally you'd then symlink that directory into the vmd directory.
This is likely the reason you're getting all of those plugin startup errors.
Once you get the directory structure fixed I'd expect the problem to go away.

I think it'd be great if you have a VMD addition to the ports tree.
The only tricky part is that due to NIH's tracking requirements, you'll
have to require them to manually download the source rather than doing
an automatic download. If you need help with anything, let me know.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Aug 12, 2004 at 11:05:49AM -0500, Stephen Montgomery-Smith wrote:
> I have managed to successfully get something compiled on FreeBSD 4.10.
> I have several questions about this process, but first I would like to
> ask more general questions.
>
> When I downloaded vmd-1.8.2.src.tar.gz and did the tar xvfz to it, it
> came up with two directories - vmd-1.8.2 and plugins. Trying to compile
> it all, it seemed to me that really plugins should be placed inside
> vmd-1.8.2, because otherwise the various compiler flags -I and -L all
> pointed to the wrong place. So (more or less) this is what I did:
>
> cd plugins
> make FREEBSD
> mv compile/lib_FREEBSD FREEBSD
> cd ../vmd-1.8.2
> mv ../plugins .
> ./configure FREEBSD OPENGL TK TCL etc etc
> cd src
> vi Makefile && vi AtomParser.C # do some requried edits
> make
> make install
>
> At the end of this process, I have installed /usr/local/bin/vmd and
> /usr/local/lib/vmd. Inside lib/vmd is plugins/FREEBSD which I think but
> am not sure if it should be there.
>
> When I run vmd, it does work, but I get a bunch of error messages - are
> these bad?
>
> The VMD sequence viewer could not be initialized properly:
> can't find package zoomseq
> AutoIMD package could not be loaded:
> can't find package autoimd
> IMD menu package could not be loaded:
> can't find package imdmenu
> Contact Map package could not be loaded:
> can't find package contactmap
> VMD PDBTool package could not be loaded:
> can't find package pdbtool
> RamaPlot package could not be loaded:
> can't find package ramaplot
> VMD RMSD package could not be loaded:
> can't find package rmsdtool
> Solvate package could not be loaded:
> can't find package solvate
> Timeline package could not be loaded:
> can't find package timeline
> VMD TkCon package could not be loaded:
> can't find package vmdtkcon
> VMD Movie Generator package could not be loaded:
> can't find package vmdmovie
>
> Finally, I see from the mailing lists that there are other FreeBSD users
> here. I would like to make it into a "port" so that all future users
> have to do is type cd /usr/ports/graphics/vmd && make install clean. I
> have already started on this, but I want to get these issues figured out
> before I work on it more.
>
>
> --
>
> Stephen Montgomery-Smith
> stephen_at_math.missouri.edu
> http://www.math.missouri.edu/~stephen 

-- 
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