VMD-L Mailing List

From: Goutham (gouthambs_at_gmail.com)
Date: Tue Mar 31 2009 - 13:34:38 CDT

Thanks John. This seems to work just fine.. I don't get any startup errors
now..

Best
Goutham

On Tue, Mar 31, 2009 at 10:21 AM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> 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/><
> > > > > 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/><
> > > 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
>