VMD-L Mailing List
From: Cheri M Turman (Cheri.M.Turman_at_uth.tmc.edu)
Date: Mon Apr 05 2004 - 12:47:54 CDT
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Hi John,
I had two linux xandros 1.0 computers with KDE 2.2 that I was trying to
install vmd on. I had checked one for different shell interpreters and
noticed that I had both sh and csh in the proper directories. I think
the problem was that I was trying to install both the vmd executable and
the vmd directory containing the other exe and libs in the smae
directory. Somehow with this one, the vmd exe was not being installed.
After sending the two to different directories, it worked.
The other computer did not have csh. I thought from the makefile that I
only needed sh. So, thank you for the tip that I needed csh. It does
seem strange that I had csh on one computer and not the other but the
one with csh is my workhorse computer for MODELLER, NAMD, AUTODOCK, etc.
Therefore, I may have needed csh for some other program and forgot that
I had installed it. Thanks again for all your help!
Cheers,
Cheri
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cheri M. Turman
Graduate Student
University of Texas-Houston Medical School
6431 Fannin
Houston, TX 77030 USA
e-mail: cheri.m.turman_at_uth.tmc.edu
Ph.: 713-500-6126
Fax: 713-500-0652
----- Original Message -----
From: John Stone <johns_at_ks.uiuc.edu>
Date: Friday, April 2, 2004 7:19 pm
Subject: Re: vmd-l: startup failure
>
> Cheri,
> Though I find it hard to imagine, it appears that your Linux
> box is _missing_ /bin/csh?????? Can you double check and tell me
> if you have a /bin/csh executable on your system? That's highly
> unusual to say the least. What version of Linux are you running?
>
> Thanks,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, Apr 02, 2004 at 03:29:00PM -0600, Cheri M Turman wrote:
> > Hi John and others,
> > I was having error messages when starting up vmd. I sent this
> question> to everyone yesterday. John Stone suggested that I was
> not installing
> > it properly since I was not seeing a special startup script
> called 'vmd'
> > and I was instead using vmd_LINUX. He was correct (thanks
> John!). I
> > am now getting the vmd script; however, I am not able to execute
> it. I
> > am getting the /bin/csh : bad interpreter error. Of course I
> thought it
> > was just a permission problem but it turns out that it is not. Any
> > ideas of how I can fix this? Below is the console where I installed
> > vmd. Is there maybe another log file stored somewhere during
> > installation which might show where an error has occured?
> >
> >
> >
> > linuxbox:~$ source ~/.bashrc
> > linuxbox:~$ ./configure
> > bash: ./configure: No such file or directory
> > linuxbox:~$ cd Desktop/vmd-1.8.2
> > linuxbox:~/Desktop/vmd-1.8.2$ ./configure
> > using configure.options: LINUX OPENGL TK TCL
> > linuxbox:~/Desktop/vmd-1.8.2$ cd src
> > linuxbox:~/Desktop/vmd-1.8.2/src$ make install
> > if [ ! -d /home/turmancm/Desktop/vmd ]; then \
> > mkdir -p /home/turmancm/Desktop/vmd ; \
> > fi ; \
> > if [ ! -d /home/turmancm/Desktop/RUNVMD ]; then \
> > mkdir -p /home/turmancm/Desktop/RUNVMD ; \
> > fi ; \
> > if [ ! -d /home/turmancm/Desktop/vmd/doc ]; then \
> > mkdir -p /home/turmancm/Desktop/vmd/doc; \
> > fi
> > cp ../Announcement /home/turmancm/Desktop/vmd
> > cp ../README /home/turmancm/Desktop/vmd
> > cp ../LICENSE /home/turmancm/Desktop/vmd
> > cp ../doc/ug.pdf /home/turmancm/Desktop/vmd/doc
> > cp ../LINUX/vmd_LINUX /home/turmancm/Desktop/vmd
> > cp ../lib/stride/stride_LINUX ../lib/surf/surf_LINUX
> > ../lib/tachyon/tachyon_LINUX /home/turmancm/Desktop/vmd
> > cd ..; tar -cf - scripts | \
> > (cd /home/turmancm/Desktop/vmd ; tar -xf -)
> > cd ../lib; tar -cf - scripts | \
> > (cd /home/turmancm/Desktop/vmd ; tar -xf -)
> > cd ..; tar -cf - python | \
> > (cd /home/turmancm/Desktop/vmd/scripts ; tar -xf -)
> > cd ..; tar -cf - plugins | \
> > (cd /home/turmancm/Desktop/vmd ; tar -xf -)
> > cp ../data/.vmdrc ../data/.vmdsensors /home/turmancm/Desktop/vmd
> > cd ../bin ; \
> > if [ -f run_vmd_tmp ]; then rm -f run_vmd_tmp; fi ; \
> > echo '#!/bin/csh' >> run_vmd_tmp ; \
> > echo 'set defaultvmddir=/home/turmancm/Desktop/vmd' >>
> run_vmd_tmp ; \
> > echo 'set vmdbasename=vmd' >> run_vmd_tmp ; \
> > cat vmd >> run_vmd_tmp ; \
> > chmod +x run_vmd_tmp ; \
> > cp run_vmd_tmp /home/turmancm/Desktop/RUNVMD/vmd ; \
> > rm -f run_vmd_tmp
> > echo Make sure /home/turmancm/Desktop/RUNVMD/vmd is in your path.
> > Make sure /home/turmancm/Desktop/RUNVMD/vmd is in your path.
> > echo "VMD installation complete. Enjoy!"
> > VMD installation complete. Enjoy!
> > linuxbox:~/Desktop/vmd-1.8.2/src$ cd ../../RUNVMD/
> > linuxbox:~/Desktop/RUNVMD$ ./vmd
> > bash: ./vmd: /bin/csh: bad interpreter: No such file or directory
> > linuxbox:~/Desktop/RUNVMD$
> >
> >
> > Thanks for any help,
> > Cheri
> > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> > Cheri M. Turman
> > Graduate Student
> > University of Texas-Houston Medical School
> > 6431 Fannin
> > Houston, TX 77030 USA
> >
> > e-mail: cheri.m.turman_at_uth.tmc.edu
> > Ph.: 713-500-6126
> > Fax: 713-500-0652
>
> Content-Description: Card for Cheri M Turman
> <Cheri.M.Turman_at_uth.tmc.edu>
>
> --
> 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
>
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- Next message: John Stone: "Re: how to make whole biological unit / virus capsid from pdb BIOMT records"
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- Maybe in reply to: John Stone: "Re: startup failure"
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