23 November 2012

280. gOpenMol on Debian Wheezy

This is a quick description of how to install gOpenMol (software for visualising output from various comp. chem. packages) on debian:

wget http://www.csc.fi/english/pages/g0penMol/Downloads/gopenmol-3.00-linux.tar.gz
tar xvf gopenmol-3.00-linux.tar.gz
sudo mv gOpenMol-3.00 /opt/
echo 'export PATH=$PATH:/opt/gOpenMol-3.00/bin' >> ~/.bashrc
source ~/.bashrc

I'm having issues with a transparent background in the main window on my nvidia box. Not sure what it's like  on other machines.


  1. Me too I have a transparent background in the main window.

  2. Me too, I have a transparent background in the main window.
    Is there someone who knows how to fix this?

  3. I've just had the same issue on Ubuntu 14.10 32bit., also an issue with being unable to type filenames in dialog boxes.

    The solution for me was to compile gOpenMol from the supplied source code (in the src/ directory). I needed to install the following libraries (plus their dependencies):

    tk8.4-dev (Tcl/Tk 8.6 didn't work)

    Hope this helps!

  4. Hi,

    I am trying to install gOpenMol-3.00 on Ubuntu-14.04. I followed your list of libraries given above.

    Checking dependencies
    dpkg -l | grep tk8.4-dev
    ii tk8.4-dev:amd64 8.4.20-7 amd64 Tk toolkit for Tcl and X11, v8.4 - development files

    dpkg -l | grep libjpeg-dev
    ii libjpeg-dev:amd64 8c-2ubuntu8 amd64 Independent JPEG Group's JPEG runtime library (dependency package)

    dpkg -l | grep python-dev
    ii libpython-dev:amd64 2.7.5-5ubuntu3 amd64 header files and a static library for Python (default)
    ii python-dev 2.7.5-5ubuntu3 amd64 header files and a static library for Python (default)

    dpkg -l | grep libglu1-mesa-dev
    ii libglu1-mesa-dev 9.0.0-2 amd64 Mesa OpenGL utility library -- development files

    dpkg -l | grep freeglut3-dev
    ii freeglut3-dev:amd64 2.8.1-1 amd64 OpenGL Utility Toolkit development files

    dpkg -l | grep bwidget
    ii bwidget 1.9.7-1 all Extension widgets for Tcl/Tk

  5. Hi
    I am trying to compile and install gOpenMOL-3.00 from source as the binary is not working.

    I checked your list of libraries given above using "dpkg -l | grep libname"

    and configured as below.
    ./configure \
    --prefix=/home/mass/MASS/TEMP/GOPENMOL/r2/gOpenMol-3.00/BIN \
    --enable-static \
    --with-mesa \
    --with-gmake \
    --with-gnu-ld \
    --with-x \
    --with-tcl=/home/mass/MASS/TEMP/GOPENMOL/TCL8420/lib \
    --with-tk=/home/mass/MASS/TEMP/GOPENMOL/TK8420/lib \
    --with-tclinclude=/home/mass/MASS/TEMP/GOPENMOL/TCL8420/include \
    CXX=gcc CC=gcc F77=f95 TCLSH=tclsh TCL_LIBRARY=/home/mass/MASS/TEMP/GOPENMOL/TCL8420/include TK_LIBRARY=/home/mass/MASS/TEMP/GOPENMOL/TK8420/include PYTHON=python

    configuration summary

    tclsh: /home/mass/MASS/TEMP/GOPENMOL/TCL8420/bin/tclsh8.4
    Tcl: -ltcl8.4g
    Tk: -ltk8.4g
    OpenGL: -lGL
    GLU: -lGLU
    glut: -lglut
    JPEG: -ljpeg
    Graphics: yes
    Plugins: yes

    make all
    make install

  6. When I try to run gopenmol I am getting
    Reading atom comversion table: /home/mass/MASS/TEMP/GOPENMOL/r2/gOpenMol-3.00/BIN/share/gOpenMol-3.00/data/atom_conversion.data ...

    Reading colour table file: colour_table.data ...
    * *
    * * * * * * g O p e n M o l * * * * * *
    * *
    * *
    * COPYRIGHT (C) Leif Laaksonen (1997-2005) *
    * *
    * Version 3.00 GNU/Linux (r. 20050923) *
    * *
    Program name: gopenmol
    Process pid: 30905
    System pagesize: 4096 (bytes)
    Tcl/Tk library version: 8.4.20
    Total size of process: 7204 (Kbytes)
    *** buffer overflow detected ***: /home/mass/MASS/TEMP/GOPENMOL/r2/gOpenMol-3.00/BIN/lib/gOpenMol-3.00/bin/gopenmol terminated

  7. kindly request for solution.

    thanks a lot