Latest revision as of 09:01, 6 June 2019

Introduction

Provides a manual binary installation of Autodock Vina on the sharcnet system for multicore use.

Usage on National Platforms (i.e. Graham, Cedar)

AutoDock Vina is an old software that has not been updated for quite a while. It depends on Boost 1.45 and relies on Boost.filesystem V2 which is deprecated (replaced by Boost.filesystme V3) and is not included in Boost 1.48 and later. The minimum Boost version available on national platforms (i.e Graham) is 1.54. As a result, AutoDock Vina is not available on national platforms as a module.

In order to run AutoDock vina on national platforms, you can download and install the binary version in your home directory using the following commands:

$ cd ~/scratch
$ wget http://vina.scripps.edu/download/autodock_vina_1_1_2_linux_x86.tgz
$ cp -av autodock_vina_1_1_2_linux_x86/bin/* ~/bin
$ rm -rf autodock_vina_1_1_2_linux_x86*

Then you can run it by 'vina':

$ vina --help

Input:
  --receptor arg        rigid part of the receptor (PDBQT)
  --flex arg            flexible side chains, if any (PDBQT)
  --ligand arg          ligand (PDBQT)

Search space (required):
  --center_x arg        X coordinate of the center
  --center_y arg        Y coordinate of the center
  --center_z arg        Z coordinate of the center
  --size_x arg          size in the X dimension (Angstroms)
  --size_y arg          size in the Y dimension (Angstroms)
  --size_z arg          size in the Z dimension (Angstroms)

Output (optional):
  --out arg             output models (PDBQT), the default is chosen based on 
                        the ligand file name
  --log arg             optionally, write log file

Misc (optional):
  --cpu arg                 the number of CPUs to use (the default is to try to
                            detect the number of CPUs or, failing that, use 1)
  --seed arg                explicit random seed
  --exhaustiveness arg (=8) exhaustiveness of the global search (roughly 
                            proportional to time): 1+
  --num_modes arg (=9)      maximum number of binding modes to generate
  --energy_range arg (=3)   maximum energy difference between the best binding 
                            mode and the worst one displayed (kcal/mol)

Configuration file (optional):
  --config arg          the above options can be put here

Information (optional):
  --help                display usage summary
  --help_advanced       display usage summary with advanced options
  --version             display program version

Usage on Legacy Systems

Version

module load autodockvina/1.1.2

Usage

Interactive

For development testing autodock vina can be run on the command line:

Example

$ vina -h

Cluster

$ sqsub -r 7d -q serial -o ofile%J vina --cpu 1 input-args

$ sqsub -r 7d -q threaded -n ncpus -o ofile%J vina --cpu ncpus input-args

Example

Coming soon ...

Graphical

Vina has no gui capability. It may however be used with MGLTOOLS https://www.sharcnet.ca/my/software/show/176

Notes

None at this time.

References

o Homepage: http://mgltools.scripps.edu/
o Manual: http://vina.scripps.edu/manual.html
o Release: http://mgltools.scripps.edu/News/
o Forum: http://vina.scripps.edu/manual.html#help