19 Dec 2010

Dock6 installation on Ubuntu Linux

What is DOCK?

DOCK addresses the problem of "docking" molecules to each other. In general, "docking" is the identification of the low-energy binding modes of a small molecule, or ligand, within the active site of a macromolecule, or receptor, whose structure is known. A compound that interacts strongly with, or binds, a receptor associated with a disease may inhibit its function and thus act as a drug. Solving the docking problem computationally requires an accurate representation of the molecular energetics as well as an efficient algorithm to search the potential binding modes.

Installation procedure

Download DOCK 6 from the official UCSF DOCK web-site and build source like this.
#########################################################
#########################################################
# Compilation procedure for Dock 6.4 on Ubuntu Linux 
#
# Date: 2010.12.19
# 
# Additional docs (where search for solutions):
# http://dock.compbio.ucsf.edu/DOCK_6/faq.htm
# http://mailman.docking.org/pipermail/dock-fans/2009-September/002247.html
#########################################################
#########################################################

#########################################################
################ install new packages ###################
sudo apt-get install flex
sudo apt-get install gfortran
sudo apt-get install byacc
#########################################################

#########################################################
################## CONFIGURE SYSTEM #####################
######
###### set gfortran as g77 (no g77 on Ubuntu)
######
cd /usr/bin/
sudo ln -s gfortran g77

######
###### Set default YACC parser to byacc
######
sudo update-alternatives --config yacc
#########################################################

#########################################################
######################## BUILD ##########################
######
###### Unpack:
######
tar -xvzf dock.6.4_source.tar.gz

######
###### Compile:
######
cd dock6/install/
./configure gnu
make clean
make 

#########################################################
######################### DONE ##########################
#########################################################
############ software is in: bin direcotry ##############
#########################################################

What to do next?

Checkout tutorials.

16 comments:

  1. hey,
    thnk for this post.
    i followed the steps but unable to run "make"
    what to do???

    ReplyDelete
  2. heloo could you help me a have an erorr after type make
    ***
    Starting installation of
    DOCK v6.5
    at pią, 11 maj 2012, 11:50:44 CEST.

    cd ../src && make install
    make[1]: Entering directory `/home/maciej/dock6/src'
    cd dock && make install
    make[2]: Entering directory `/home/maciej/dock6/src/dock'
    g++ -c -O2 -o filter.o filter.cpp
    make[2]: g++: Command not found
    make[2]: *** [filter.o] Error 127
    make[2]: Leaving directory `/home/maciej/dock6/src/dock'
    make[1]: *** [dock6] Error 2
    make[1]: Leaving directory `/home/maciej/dock6/src'
    make: *** [install] Error 2

    ReplyDelete
  3. Maciej, you should first install build-essentials like this:

    apt-get install build-essential

    and later try to run ./configure gnu ; make clean ; make ; make install

    Have fun! :)

    ReplyDelete
    Replies
    1. thank you very much it works could you have some tutorials for beginers ????

      Delete
    2. Maybe someday, but it won't be anytime soon. There should be some tutorials on official Dock6 website - try it, or find other on Google ;).

      Delete
  4. i have sucessfully installed dock6 on ubuntu according to your suggestion but when i open the terminal and type dock6 it doesn't recognize the command .my dock6 directory is on Desktop and have install the docking program from there. when i execute the command dock6 from /Desktop/dock6/bin/directory than it work.
    could you tell me how i can set the envirnment so that i can use the dock from any directory

    ReplyDelete
    Replies
    1. Ok, you should, add this line to your ~/.bashrc:


      export PATH="~/Desktop/dock6/bin:${PATH}"


      If you are using Bash, it will be the most optimal way.

      Delete
  5. i am having a different issue i have installed dock6 as per the details given above now when i go into my bin folder and try run i get this error :
    Usage:
    dock6 -i filename.in [-o filename.out] [-v]

    please help me out ...

    ReplyDelete
    Replies
    1. Hello,

      So you have dock6 compiled and ready to use - how you will use it it's up to you :). I haven't used this software for long time, so I really don't remember what swhitches are most common. Please reffer to documentation.

      Have a nice day! :)

      Delete
  6. Thanks for ur help. i was able to install as per ur instruction in a giffy. :)

    ReplyDelete
  7. Construct box to enclose spheres
    ../../../bin/showbox < box.in > /dev/null
    /bin/sh: 1: ../../../bin/showbox: not found
    make[3]: *** [showbox] Error 127
    make[3]: Leaving directory `/home/abdul/dock6/install/test/grid_generation'
    make[2]: *** [grid_generation] Error 2
    make[2]: Leaving directory `/home/abdul/dock6/install/test/bump_filter'
    make[1]: *** [sampling] Error 2
    make[1]: Leaving directory `/home/abdul/dock6/install/test'
    make: *** [timed_test] Error 2


    Please help me in this error.

    ReplyDelete
  8. Hi!

    I don't have idea what is wrong with your installation. Two months ago I've created Dock6 Docker container you can use it. Project is hosted on github: https://github.com/0x1fff/docker-dock6 you can try to use it.

    ReplyDelete
  9. hi.i am a milad .plaese help me
    how to sole error install dock 6 :::

    cd ../src/dock && make install
    make[1]: Entering directory `/home/molecular/dock6/src/dock'
    g++ -c -O2 -o amber_typer.o amber_typer.cpp
    make[1]: g++: Command not found
    make[1]: *** [amber_typer.o] Error 127
    make[1]: Leaving directory `/home/molecular/dock6/src/dock'
    make: *** [dock] Error 2

    ReplyDelete
    Replies
    1. You can run: sudo apt-get install build-essential - it will download you g++ compiller, but I recommend you to use my pet project that I've created few months ago Dock6 Docker container. Project is hosted on github: https://github.com/0x1fff/docker-dock6 - just try it :). It will create Debian package with Dock6, or you will be able to use it from Docker container.

      Delete
  10. hi any body
    i'm milad
    step by step exact compile DOCK6 on ubuntu:

    1- sudo apt-get update
    2- sudo apt-get install flex
    3- sudo apt-get install gfortran
    default g77 as below:
    cd /usr/bin/
    sudo ln -s gfortran g77

    4- sudo apt-get install byacc
    Set default YACC parser to byacc
    sudo update-alternatives --config yacc

    5-apt-get install build-essential

    Install dock6
    1- untar dock6-suite as below
    tar -xzvf dock6
    2-change directory to install folder
    ./configure
    make clean
    make all
    make test
    make check
    make install
    3- export bin direcctory as below
    export PATH="/home/molecular/ProgramFiles/dock6/bin:${PATH}"

    ReplyDelete