Introduction

The VMD software is available from the Theoretical and Computational Biophysics Group at the University of Illinois at Urbana-Champaign. http://www.ks.uiuc.edu/Research/vmd/

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.

VMD provides a sequence plugin which can be used to view a structure's sequence, secondary structure code, and B value in a scrolling window. The sequence viewer can zoom in on a region of interest, and selections can be made on the sequence, which are then highlighted on the structure in VMD's OpenGL graphics window.

https://biocore-s.ks.uiuc.edu/biocore/

Usage

module load vmd/1.9.1a17

Installation

module load cuda/4.0

mkdir -p /sw/vmd/1.9.1a17/src
cd /sw/vmd/1.9.1a17/src
tar -zxvf vmd-1.9.1a17.bin.LINUX.opengl.tar.gz
cd vmd-1.9.1a17
pwd
/sw/vmd/1.9.1a17/src/vmd-1.9.1a17

Edit the file 'configure'; change the values for the $install_library_dir and $install_bin_dir to a directory in which vmd data files and executables should be installed

$install_bin_dir is the location of the startup script 'vmd'. It should be located in the path of users interested in running VMD.

($install_library_dir="/sw/vmd/1.9.1a17/lib/$install_name";"; AND $install_bin_dir="/sw/vmd/1.9.1a17/bin"; )
./configure

(using configure.options: LINUX OPENGL FLTK TK ACTC CUDA IMD LIBSBALL XINERAMA XINPUT LIBTACHYON VRPN NETCDF TCL PTHREADS SILENT ICC)
cd src
make install
(Make sure /sw/vmd/1.9.1a17/bin/vmd is in your path.
VMD installation complete. Enjoy! )

When installed, type 'vmd' to start

module file

 module display vmd/1.9.1a17
-------------------------------------------------------------------
/sw/com/modulefiles/vmd/1.9.1a17:

module           load cuda/4.0
prepend-path     LD_LIBRARY_PATH /sw/vmd/1.9.1a17/lib/vmd
prepend-path     PATH /sw/vmd/1.9.1a17/bin
-------------------------------------------------------------------

Dependency

Needed for software "Desmond"

post install

rpm -ivh mesa-libGLU-7.11-5.el6.i686.rpm mesa-libGL-7.11-5.el6.i686.rpm 
rpm -ivh libXdamage-1.1.2-1.el6.i686.rpm
rpm -ivh libXxf86vm-1.1.0-1.el6.i686.rpm
rpm -ivh mesa-dri-drivers-7.11-5.el6.i686.rpm expat-2.0.1-11.el6_2.i686.rpm
rpm -Uvh libdrm*rpm
rpm -ivh mesa-libGLU-7.11-5.el6.i686.rpm mesa-libGL-7.11-5.el6.i686.rpm
rpm -ivh libXinerama-1.1-1.el6.i686.rpm
rpm -ivh libXi-1.3-3.el6.i686.rpm
rpm -ivh libXrender-0.9.5-1.el6.i686.rpm
rpm -ivh freetype-2.3.11-6.el6_2.9.i686.rpm
rpm -ivh fontconfig-2.8.0-3.el6.i686.rpm
rpm -ivh libXft-*rpm
rpm -ivh libXft-2.1.13-4.1.el6.i686.rpm

Reference

1. https://biocore-s.ks.uiuc.edu/biocore/

2. https://biocore-s.ks.uiuc.edu/biocore/secure/biofs/biofs.do?directory=/VMD%20(Public)/alpha/