Thursday, November 08, 2012

Installing DOCK 6.1 on mint linux

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
     --> 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=
     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.

Monday, November 05, 2012

Adding PATH of directory in mint linux

I spent several hours trying to figure this out. There are so many resources in the internet that it is often difficult to get what we really need. I am writing it down here in case I forget again one day (or if anybody is experiencing the same problem).

Some suggested modifying the .bashrc files, some suggested to modify the etc/profile file, but what worked for me was by modifying the "environment" file. I just searched for the environment file using the search facility of mint linux's finder, then modify it by adding my directory path. 

From PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" 



 Logged out, logged back in, and I was able to execute all the files within my target directory. Nothing fancy, but it worked out for me.