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
gopenmol-3.00-linux.tar.gz
tar xvf gopenmol-3.00-linux.tar.gz
sudo mv gOpenMol-3.00 /opt/
/opt/gOpenMol-3.00/./install
echo 'export PATH=$PATH:/opt/gOpenMol-3.00/bin' >> ~/.bashrc
source ~/.bashrc
rungOpenMol
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.
Lindqvist - a blog about Linux and Science. Mostly.
Me too I have a transparent background in the main window.
ReplyDeleteMe too, I have a transparent background in the main window.
ReplyDeleteIs there someone who knows how to fix this?
oh
I've just had the same issue on Ubuntu 14.10 32bit., also an issue with being unable to type filenames in dialog boxes.
ReplyDeleteThe 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)
libjpeg-dev
python-dev
libglu1-mesa-dev
freeglut3-dev
bwidget
Hope this helps!
Hi,
ReplyDeleteI 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
Hi
ReplyDeleteI 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.
#!/bin/bash
./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 \
--with-tkinclude=/home/mass/MASS/TEMP/GOPENMOL/TK8420/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
Python:
Graphics: yes
Plugins: yes
make all
make install
When I try to run gopenmol I am getting
ReplyDeleteReading atom comversion table: /home/mass/MASS/TEMP/GOPENMOL/r2/gOpenMol-3.00/BIN/share/gOpenMol-3.00/data/atom_conversion.data ...
done
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
kindly request for solution.
ReplyDeletethanks a lot