Autodock4.2 and autodockvina112

Usage

module load autodock/autodock423     
module load autodock/autodockvina112

compilation

% ./configure    (* see below)
 % make
 % make test   ( optional, recommended, requires "python")
 % make install


./configure --prefix=/sw/autodock/autodock42/ 

./configure --prefix=/sw/autodock/autodock42/
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for gawk... (cached) gawk
checking for g++... g++
checking for C++ compiler default output file name... a.out
checking whether the C++ compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of g++... gcc3
checking for a BSD-compatible install... /usr/bin/install -c
checking for ranlib... ranlib
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking dependency style of gcc... gcc3
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E

make
make test
make install

module files

 more autodock423
#%Module######################################################################
##
##      autodock41
##
proc ModulesHelp { } {
        puts stderr "Sets up environment to use autodock 4.2.3"
}

set base        /sw/autodock
set vers        autodock423

set-alias autodock       $base/$vers/bin/autodock4
set-alias autogrid       $base/$vers/bin/autogrid4
prepend-path    PATH    $base/$vers/bin

more autodockvina112
#%Module######################################################################
##
##      autodock_vina_1_1_2
##
proc ModulesHelp { } {
        puts stderr "Sets up environment to use autodock_vina_1_1_2 "
}

set base        /sw/autodock/autodockvina/
set vers        autodock_vina_1_1_2

set-alias vina       $base/$vers/bin/vina
set-alias vina_split $base/$vers/bin/vina_split
prepend-path    PATH    $base/$vers/bin

MGLTools 1.5.4 (autodocktools)

http://mgltools.scripps.edu/ http://mgltools.scripps.edu/downloads http://mgltools.scripps.edu/documentation

Usage

 module load autodock/mgltools1.5.4

To run python commands you need to pythonsh

pythonsh filename.py

Installation Directory

/sw/autodock/MGLTools/1.5.4

compilation

module load autodock/autodock423     
module load autodock/autodockvina112
mkdir -p /sw/autodock/MGLTools/1.5.4/src
cd /sw/autodock/MGLTools/1.5.4/src
cp SOURCEFILES /sw/autodock/MGLTools/1.5.4/src
tar -zxvf mgltools_x86_64Linux2_1.5.4.tar.gz
cd /sw/autodock/MGLTools/1.5.4/src/mgltools_x86_64Linux2_1.5.4

 ./install.sh -d /sw/autodock/MGLTools/1.5.4 -c 1 2>&1 |tee mgltools_install.txt
The installation script installs MGLTools in
        InstDir/MGLToolsPckgs .

        It also creates various shell scripts (pmv, adt, vision, pythonsh)
        in InstDir/bin.


 MGLTools installation complete.
To run pmv, adt, vision or pythonsh scripts located at:
/sw/autodock/MGLTools/1.5.4/bin
you will need to do ONE of the following:

-- add the /sw/autodock/MGLTools/1.5.4/bin to the path environment variable in .cshrc or .bashrc:
.cshrc:
set path = (/sw/autodock/MGLTools/1.5.4/bin $path)

.bashrc
export PATH=/sw/autodock/MGLTools/1.5.4/bin:$PATH

-- create aliases in your .cshrc or .bashrc
.cshrc:
alias pmv /sw/autodock/MGLTools/1.5.4/bin/pmv
alias adt /sw/autodock/MGLTools/1.5.4/bin/adt
alias vision /sw/autodock/MGLTools/1.5.4/bin/vision
alias pythonsh /sw/autodock/MGLTools/1.5.4/bin/pythonsh

.bashrc
alias pmv='/sw/autodock/MGLTools/1.5.4/bin/pmv'
alias adt='/sw/autodock/MGLTools/1.5.4/bin/adt'
alias vision='/sw/autodock/MGLTools/1.5.4/bin/vision'
alias pythonsh='/sw/autodock/MGLTools/1.5.4/bin/pythonsh'


If you have any problems please visit our FAQ page (http://mgltools.scripps.edu/documentation/faq).

module files

 module display autodock/mgltools1.5.4
-------------------------------------------------------------------
/sw/com/modulefiles/autodock/mgltools1.5.4:

set-alias        pmv /sw/autodock/MGLTools/1.5.4/bin/pmv
set-alias        adt /sw/autodock/MGLTools/1.5.4/bin/adt
set-alias        vision /sw/autodock/MGLTools/1.5.4/bin/vision
set-alias        pythonsh /sw/autodock/MGLTools/1.5.4/bin/pythonsh
prepend-path     PATH /sw/autodock/MGLTools/1.5.4/bin
-------------------------------------------------------------------