VMD-L Mailing List

From: Lorenzo Isella (lorenzo.isella_at_gmail.com)
Date: Wed Oct 03 2007 - 07:48:08 CDT

Dear All,

I am struggling to get the VMD software installed on my laptop running
Debian testing.
In the following I give a detailed account of what I did.
I need VMD to get started with the molecular dynamics software
Espresso (http://espressowiki.mpip-mainz.mpg.de/wiki/index.php/Main_Page).
I downloaded and untarred VMD, moving the plugin directory into
the newly created vmd directory.
Then here is what I did:

iselllo_at_cappero:~/internet-download/vmd-1.8.6$ ./configure
using configure.options: WIN32 TCL
iselllo_at_cappero:~/internet-download/vmd-1.8.6$ make
VMD Build Options
-----------------
 Hardware accelerated versions:
     aix4.opengl - AIX 4.3
     aix5.opengl - AIX 5
  aix5.64.opengl - AIX 5, 64-bit
   hpux11.opengl - HP-UX 11.0
    irix6.opengl - IRIX 6.5.x
 irix6.64.opengl - IRIX 6.5.x, 64-bit
    linux.opengl - Redhat Linux (32-bit)
    linux.cuda.opengl - Redhat Linux (32-bit), NVIDIA CUDA
    linux.amd64.opengl - Redhat Linux (64-bit)
    linux.ia64.opengl - Redhat Linux Itanium EL3 (64-bit)
   macosx.opengl - MacOS X 10.2
   macosx.opengl.x11 - MacOS X 10.3
  solaris.opengl - Solaris 9
solaris.64.opengl - Solaris 9, 64-bit
    tru64.opengl - Tru64 Unix 4.0F

 Non-accelerated versions:
       aix4.mesa - AIX 4.3
    freebsd.mesa - FreeBSD 5.x
     hpux11.mesa - HP-UX 11.0
      linux.mesa - Redhat Linux 7.x
 linuxalpha.mesa - Linux/Alpha
   linuxppc.mesa - Linux/PowerPC
     macosx.mesa - MacOS X 10.1
    solaris.mesa - Solaris 8
      tru64.mesa - Tru64 Unix 4.0F
-----------------------------------------------
Type 'make platform' to configure VMD for any of
the target platforms listed above.

Once VMD is configured for compilation, do this:
 cd src; make veryclean; make

iselllo_at_cappero:~/internet-download/vmd-1.8.6$ make platform
make: *** No rule to make target `platform'. Stop.
iselllo_at_cappero:~/internet-download/vmd-1.8.6$ cd s
scripts/ shaders/ src/
iselllo_at_cappero:~/internet-download/vmd-1.8.6$ cd s
scripts/ shaders/ src/
iselllo_at_cappero:~/internet-download/vmd-1.8.6$ cd src/
iselllo_at_cappero:~/internet-download/vmd-1.8.6/src$ make veryclean
cd ../WIN32 ; \
               rm -f *.o *.warnings *.depend.old core
rm -f vmd_python.C vmd.py
cd ../WIN32 ; \
         rm -rf ; \
         rm -f vmd_WIN32
cd ../src ; \
         rm -f *.o *.a *~ core; \
         rm -rf ; \
         rm -f vmd_WIN32
cd ../doc ; \
         rm -f *~ core
iselllo_at_cappero:~/internet-download/vmd-1.8.6/src$ sudo checkinstall

checkinstall 1.6.1, Copyright 2002 Felipe Eduardo Sanchez Diaz Duran
          This software is released under the GNU GPL.

The package documentation directory ./doc-pak does not exist.
Should I create a default set of package docs? [y]:

Preparing package documentation...OK

*** No known documentation files were found. The new package
*** won't include a documentation directory.

Please write a description for the package.
End your description with an empty line or EOF.
>> new attempt to build vmd
>>

*****************************************
**** Debian package creation selected ***
*****************************************

This package will be built according to these values:

0 - Maintainer: [ root_at_cappero.jrc.it ]
1 - Summary: [ new attempt to build vmd ]
2 - Name: [ src ]
3 - Version: [ 20071002 ]
4 - Release: [ 1 ]
5 - License: [ GPL ]
6 - Group: [ checkinstall ]
7 - Architecture: [ i386 ]
8 - Source location: [ src ]
9 - Alternate source location: [ ]
10 - Requires: [ ]

Enter a number to change any of them or press ENTER to continue:

Installing with make install...

========================= Installation results ===========================
if [ ! -d "/usr/local/lib/vmd" ]; then \
               mkdir -p "/usr/local/lib/vmd" ; \
       fi ; \
       if [ ! -d "/usr/local/bin" ]; then \
               mkdir -p "/usr/local/bin" ; \
       fi ; \
       if [ ! -d "/usr/local/lib/vmd"/doc ]; then \
               mkdir -p "/usr/local/lib/vmd"/doc; \
       fi
cp ../Announcement "/usr/local/lib/vmd"
cp ../README "/usr/local/lib/vmd"
cp ../LICENSE "/usr/local/lib/vmd"
cp ../doc/ug.pdf "/usr/local/lib/vmd"/doc
if [ -f /usr/local/lib/vmd/vmd_WIN32 ]; then \
          mv -f "/usr/local/lib/vmd/vmd_WIN32"
"/usr/local/lib/vmd/OLD_vmd_WIN32" ; rm -f
"/usr/local/lib/vmd/OLD_vmd_WIN32" ; fi
cp ../WIN32/vmd_WIN32 "/usr/local/lib/vmd"
cp: cannot stat `../WIN32/vmd_WIN32': No such file or directory
make: [install] Error 1 (ignored)
cp ../lib/stride/stride_WIN32 ../lib/surf/surf_WIN32
../lib/tachyon/tachyon_WIN32 "/usr/local/lib/vmd"
cp: cannot stat `../lib/stride/stride_WIN32': No such file or directory
cp: cannot stat `../lib/surf/surf_WIN32': No such file or directory
cp: cannot stat `../lib/tachyon/tachyon_WIN32': No such file or directory
make: [install] Error 1 (ignored)
cd ..; tar -cf - scripts | \
       (cd "/usr/local/lib/vmd" ; tar -xf -)
cd ../lib; tar -cf - scripts | \
       (cd "/usr/local/lib/vmd" ; tar -xf -)
cd ..; tar -cf - python | \
       (cd "/usr/local/lib/vmd"/scripts ; tar -xf -)
cd ..; tar -cf - plugins | \
       (cd "/usr/local/lib/vmd" ; tar -xf -)
cd ..; tar -cf - shaders | \
       (cd "/usr/local/lib/vmd" ; tar -xf -)
cp ../data/.vmdrc ../data/.vmdsensors "/usr/local/lib/vmd"
cd ../bin ; \
       if [ -f run_vmd_tmp ]; then rm -f run_vmd_tmp; fi ; \
       echo '#!/bin/csh' >> run_vmd_tmp ; \
       echo 'set defaultvmddir="/usr/local/lib/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 "/usr/local/bin"/vmd ; \
       rm -f run_vmd_tmp
echo Make sure "/usr/local/bin"/vmd is in your path.
Make sure /usr/local/bin/vmd is in your path.
echo "VMD installation complete. Enjoy!"
VMD installation complete. Enjoy!

======================== Installation successful ==========================
grep: /var/tmp/DgbJQLofilokkYaqGZZZP/newfile: No such file or directory

Copying files to the temporary directory...OK

Striping ELF binaries and libraries...OK

Compressing man pages...OK

Building file list...OK

Building Debian package...OK

Installing Debian package...OK

Erasing temporary files...OK

Writing backup package...OK

Deleting temp dir...OK

**********************************************************************

 Done. The new package has been installed and saved to

 /home/iselllo/internet-download/vmd-1.8.6/src/src_20071002-1_i386.deb

 You can remove it from your system anytime using:

     dpkg -r src

**********************************************************************

Again sorry for the long post. So, somehow, I got VMD installed successfully.
Then I tried re-running the tutorial (a TCL script) this time using VMD for
visualization.
The part of the TCL script needing VMD is in the following:

# 6 Visualization #
# Now lets see what you have done so far. #
# Set the variable vmd to "yes" for trying. #
# TCL: #
# Here you can already see how an 'if' condition works in #
# tcl. #
#############################################################

set vmd "yes"

if { $vmd == "yes" } {
# This calls a small tcl script which starts the program #
# VMD and opens a socket connection between ESPResSo and #
# VMD. #
    prepare_vmd_connection tutorial 3000

# Just wait a moment until VMD has started. #
# The 'exec' command is quite useful since with that you can#
# call any other program from within your simulation script.#
    exec sleep 4

# The additional command imd steers the socket connection #
# to VMD, e.g. sending the actual coordinates #
    imd positions
}

, but here is what happened when I ran the script; an xterm terminal opened with
the message:

xterm: Can't execvp /usr/local/lib/vmd/vmd_LINUX: No such file or directory

In fact this is the content of the folder which is giving me some headache:

 ls /usr/local/lib/vmd/
Announcement doc LICENSE plugins README scripts shaders

Can anyone help me out? I am sure there must be other Debian/Ubuntu
users or simply people building from source who went through
this...and I am also sure that if has to be rather trivial to sort
this out, for someone knowledgeable.
Many thanks