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Latest revision as of 09:01, 6 June 2019
This page is scheduled for deletion because it is either redundant with information available on the CC wiki, or the software is no longer supported. |
Contents
AUTODOCKVINA |
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Description: Open source molecular modelling docking program., |
SHARCNET Package information: see AUTODOCKVINA software page in web portal |
Full list of SHARCNET supported software |
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