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Compiling AutoDock Vina

AutoDock Vina is an open-source program for doing molecular docking.[1]

Documentation

Official documentation: https://autodock-vina.readthedocs.io/en/latest/introduction.html

Source Code

GitHub repository: https://github.com/ccsb-scripps/AutoDock-Vina

Compilation

See official build instructions.

We will use:

  • Intel compilers via Intel Composer XE
  • Boost 1.75.0
  • Python 3.7.7 provided by Intel Composer XE (optional)

Load the appropriate modulefiles:

  • intel/composerxe/2020u4
  • boost/intel/2020/1.75.0

Get source from: https://github.com/ccsb-scripps/AutoDock-Vina/releases

Expand archive:

[juser@picotte001 ~]$ cd /ifs/groups/myrsrchGrp/src
[juser@picotte001 ~]$ tar -xf v1.2.3.tar.gz

which creates the directory AutoDock-Vina-1.2.3

Install Location

We will install the executables to a subdirectory of your group directory. First, create the directory structure:

[juser@picotte001 ~]$ cd /ifs/groups/myrsrchGrp
[juser@picotte001 ~]$ mkdir -p software/bin

Modify Makefile

We will modify the Makefile to use the Intel Compiler, and set optimization options. We also set installation location.

[juser@picotte001 ~]$ cd AutoDock-Vina-1.2.3/build/linux/release
[juser@picotte001 release]$

Edit the Makefile to look like this:

BASE=/ifs/groups/myrsrchGrp/software/
BOOST_VERSION=
BOOST_INCLUDE = $(BASE)/include
C_PLATFORM=-pthread
GPP=icpc
C_OPTIONS= -O3 -DNDEBUG -std=c++11 -xHost
BOOST_LIB_VERSION=

include ../../makefile_common

Compile

We compile with 12 concurrent processes, and redirect output to a file so we can inspect it later.

[juser@picotte001 release]$ make -j 12 | tee Make.out 2>&1

This generates a bunch of .o files and the two executables vina and vina_split.

There is no installer, so copy the executables to an appropriate location.

[juser@picotte001 release]$ cp vina vina_split /ifs/groups/myrsrchGrp/software/bin

Using Vina

In order to use Vina, you will need to add /ifs/groups/myrsrchGrp/software/bin to your PATH environment variable.

References

[1] AutoDock Vina website