VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Mar 31 2009 - 12:21:00 CDT

Goutham,
  You can't just extract the tar file and run the code without
actually installing it, that's why you're getting the errors you
mention below. You need to install it somewhere, though you can
install it in any directory you like, including /tmp. Once it is
installed correctly, the startup errors you were getting will go away.
See the top of the 'configure' script to see how to override the default
installation target directories.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Mar 31, 2009 at 10:15:57AM -0700, Goutham wrote:
> Hey John,
>
> Thanks for the text build. I extracted VMD in my local directory to test if
> it will work independently. I got a few errors.
>
> 1) It did not have the correct tcl folder to look for init.tcl. I put an
> entry in the .vmdrc but didn't help. So I just copied the tcl directory into
> the place where it was looking for which fixed it. (guess adding path is a
> better way, but where do I add?)
>
> Now vmd is looking for vmdinit.tcl, colordefs.dat etc in:
> /usr/local/lib/vmd/scripts/vmd
>
> I want to change the path to the path in my home directory. How do I do
> that?
>
> THanks
> Goutham
>
>
> On Tue, Mar 31, 2009 at 9:38 AM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> > Goutham,
> > I've built a text-only VMD for you and placed it in the alpha test
> > directory for you, accessible by following the instructions here:
> > http://www.ks.uiuc.edu/Research/vmd/alpha/
> >
> > You want the file named:
> > vmd-1.8.7a63.bin.LINUX.text.tar.gz
> >
> > Give that a try and let me know how it goes for you.
> >
> > Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Sun, Mar 29, 2009 at 12:45:45PM -0700, Goutham wrote:
> > > Hey John,
> > > I tried including the path for the openGL library. But it doesn't work in
> > > our cluster. I am trying to see if that can be fixed. Meanwhile, it will
> > be
> > > helpful if you can tell me how to get a text only build of VMD. If you
> > tell
> > > us how to modify the makefile to compile into a text only build, then we
> > can
> > > build it ourselves.
> > >
> > > Thanks
> > > Goutham
> > >
> > >
> > >
> > >
> > > On Fri, Mar 27, 2009 at 5:53 AM, John Stone <johns_at_ks.uiuc.edu> wrote:
> > >
> > > >
> > > > Goutham,
> > > > No, one can't "include" these commands via tclsh, as they are part
> > > > of the compiled VMD code, and not a script. You'll need to take one of
> > > > the approaches that were previously described.
> > > >
> > > > Cheers,
> > > > John Stone
> > > > vmd_at_ks.uiuc.edu
> > > >
> > > > On Thu, Mar 26, 2009 at 11:34:00PM -0700, Goutham wrote:
> > > > > Hey John,
> > > > > Thanks for ur response. I thot of another approach. I use very few
> > vmd
> > > > tcl
> > > > > commands, like "mol load pdb " and writepdb in my tcl script. So is
> > it
> > > > > possible to just "inlcude" these select "packages" and just run the
> > tcl
> > > > > script using tclsh.
> > > > >
> > > > > Do you know if I can do this? Are these functions available as
> > > > executables
> > > > > or tcl packages?
> > > > >
> > > > > Thanks
> > > > > Goutham
> > > > >
> > > > >
> > > > > On Thu, Mar 26, 2009 at 7:38 PM, John Stone <johns_at_ks.uiuc.edu>
> > wrote:
> > > > >
> > > > > > Hi,
> > > > > > In addition to copying the shared library(ies) as already
> > > > > > suggested by Axel, one can compile VMD from source in a text-only
> > > > > > build that doesn't need the OpenGL libraries. I'd suggest trying
> > > > > > Axel's suggestion first, but if you are unable to get that working,
> > > > > > I can provide you with a text only build of VMD next week when I
> > > > > > return from travelling.
> > > > > >
> > > > > > Cheers,
> > > > > > John Stone
> > > > > > vmd_at_ks.uiuc.edu
> > > > > >
> > > > > > On Thu, Mar 26, 2009 at 05:48:52PM -0700, Goutham wrote:
> > > > > > > Hey,
> > > > > > > I am using qsub script to launch a vmd command such as:
> > > > > > >
> > > > > > > "vmd -dispdev text < script.tcl"
> > > > > > >
> > > > > > > However I get the following error:
> > > > > > > libGLU.so.1: cannot open shared object file...
> > > > > > >
> > > > > > > It is my understanding that the openGL library is not available
> > in
> > > > the
> > > > > > > individual nodes in the cluster. However I would guess that since
> > i
> > > > am
> > > > > > doing
> > > > > > > the "text" option, the openGL library should not be required. Is
> > > > there a
> > > > > > way
> > > > > > > to disable this?
> > > > > > >
> > > > > > > Can anyone tell me what my options are otherwise?
> > > > > > >
> > > > > > > Thanks
> > > > > > > Goutham
> > > > > >
> > > > > > --
> > > > > > 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/>
> > <http://www.ks.uiuc.edu/%7Ejohns/><
> > > > http://www.ks.uiuc.edu/%7Ejohns/>
> > > > > > Fax: 217-244-6078
> > > > > >
> > > >
> > > > --
> > > > 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/><
> > http://www.ks.uiuc.edu/%7Ejohns/>
> > > > Fax: 217-244-6078
> > > >
> >
> > --
> > 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/ <http://www.ks.uiuc.edu/%7Ejohns/>
> > Fax: 217-244-6078
> > 

-- 
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