VMD-L Mailing List

From: Goutham (gouthambs_at_gmail.com)
Date: Tue Mar 31 2009 - 12:15:57 CDT

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
>