HOW_TO_INSTALL

################ INSTALLATION ###################

# The user can extract the source code in some location, i.e. /home/myprogram/, by typing 

tar zxvf GMXPBSAtool.tar.gz; 

# set the GMXPBSAHOME environment variable in bash: 

export GMXPBSAHOME=/home/myprogram/GMXPBSAtool 

# Change the /home/myprogram to whatever directory is appropriate for your machine, verify that you have write permissions in the directory tree, 
# and that the gmxpbsa0.sh, gmxpbsa1.sh and gmxpbsa2.sh scripts have execute permissions. $GMXPBSAHOME should be also added to the PATH.
# GMXPBSAtool uses bash environment. So make sure that you are in the bash shell (echo $SHELL should give /bin/bash). To use bash shell just type

bash 

# Ubuntu and Debian derived make use of dash shell rather than bash. We force GMXPBSAtool to use bash but if you encounter problem in 
# running the tool check whether bash shell is installed.


################ APBS and GROMACS ###################

# In order to perform the MM/PBSA calculation, APBS program (http://www.poissonboltzmann.org/apbs/) and 
# GROMACS tool (www.gromacs.org) must be installed and working. 
# In Ubuntu/Xubuntu/Kubuntu and Debian derived you can install them by:

sudo apt-get install apbs
sudo apt-get install gromacs

# Make sure that you are using the latest updated version of APBS and GROMACS version 4.5 and later. Both programs can be installed by compiling 
# the source code too, without root permission.


################ HOW TO RUN GMXPBSAtool ###################

# In order to perform the MM/PBSA calculation,the user has to run the tool by typing $GMXPBSAHOME/<script>, where <script> can be either gmxpbsa0.sh,
# or gmxpbsa1.sh or gmxpbsa2.sh depending on  stage of the calculation that will be performed (see section 2.4 of the paper). 
# Each script will read the INPUT.dat file to perform the MM/PBSA calculation. 
# For instance, if the INPUT.dat file and the simulations are located in /home/mysimulations, 
# in this directory the user can run the tool typing $GMXPBSAHOME/<script>. See section 3 of the paper for further details or the DEMO examples