For people who are new to the UNIX system, installing programs manually can be a daunting task. This was indeed the case for me anyway. I needed to install some molecular modeling softwares such as GROMACS and DOCK from UCSF, and I had a hard time doing so.
For GROMACS, it was a straight forward task, as it was available in the mint linux repository, and other important components for the installation was automatically added. It wasn't so for DOCK 6.1, because I needed to install it manually and prepare the prerequisites as well, and I had to go through many trial and errors.
After googling and looking into several forums, I finally got DOCK 6.1 to work on my virtual mint linux (installed in windows 7). The summary of the procedures that I did, from unpacking to installing DOCK is as follows:
tar -zxvf dock.6.1_source.tar.gz
cd dock6
cd install
su
--> input root password
In order to install the required compilers and other prerequisites, I needed to run apt-get. Unfortunately, because I am behind a campus proxy, I wasn't able to do it normally, so I had to find a way around it.
-->(in su mode)
export http_proxy=http://proxy.campus.net:8080
apt-get install build-essential flex bison gfortran
--> change g77 to gfortran
--> go to the /usr/bin/ directory
cd /usr/bin/
ln -s gfortran g77
--> go to the dock6/install/ directory
./configure gnu
make all
--> in case of any "error: 'strlen' was not declared in this scope" errors, insert following lines in the mentioned .cpp files using a text editor:
#include "cstdlib"
#include "string.h"
--> Finish the DOCK installation
This did the trick for me, and thank God, I am now able to run docking simulations using DOCK with no hassle.
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