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autodock_vina

About

AutoDock is an open-source program for doing molecular docking, significantly improves the average accuracy of the binding mode predictions compared to AutoDock 4

Versions and Availability

▶ Display Softenv Keys for autodock_vina on all clusters
Machine Version Softenv Key
supermike2 1.1.2 +autodock_vina-1.1.2
▶ Softenv FAQ?

The information here is applicable to LSU HPC and LONI systems.

Softenv

SoftEnv is a utility that is supposed to help users manage complex user environments with potentially conflicting application versions and libraries.

System Default Path

When a user logs in, the system /etc/profile or /etc/csh.cshrc (depending on login shell, and mirrored from csm:/cfmroot/etc/profile) calls /usr/local/packages/softenv-1.6.2/bin/use.softenv.sh to set up the default path via the SoftEnv database.

SoftEnv looks for a user's ~/.soft file and updates the variables and paths accordingly.

Viewing Available Packages

Using the softenv command, a user may view the list of available packages. Currently, it can not be ensured that the packages shown are actually available or working on the particular machine. Every attempt is made to present an identical environment on all of the LONI clusters, but sometimes this is not the case.

Example,

$ softenv
These are the macros available:
*   @default
These are the keywords explicitly available:
+amber-8                       Applications: 'Amber', version: 8 Amber is a
+apache-ant-1.6.5              Ant, Java based XML make system version: 1.6.
+charm-5.9                     Applications: 'Charm++', version: 5.9 Charm++
+default                       this is the default environment...nukes /etc/
+essl-4.2                      Libraries: 'ESSL', version: 4.2 ESSL is a sta
+gaussian-03                   Applications: 'Gaussian', version: 03 Gaussia
....
Listing of Available Packages

See Packages Available via SoftEnv on LSU HPC and LONI.

For a more accurate, up to date list, use the softenv command.

Caveats

Currently there are some caveats to using this tool.

  1. packages might be out of sync between what is listed and what is actually available
  2. resoft and soft utilities are not; to update the environment for now, log out and login after modifying the ~/.soft file.
Availability

softenv is available on all LSU HPC and LONI clusters to all users in both interactive login sessions (i.e., just logging into the machine) and the batch environment created by the PBS job scheduler on Linux clusters and by loadleveler on AIX clusters..

Packages Availability

This information can be viewed using the softenv command:

% softenv
Managing Environment with SoftEnv

The file ~/.soft in the user's home directory is where the different packages are managed. Add the +keyword into your .soft file. For instance, ff one wants to add the Amber Molecular Dynamics package into their environment, the end of the .soft file should look like this:

+amber-8

@default

To update the environment after modifying this file, one simply uses the resoft command:

% resoft
▶ Display Module Names for autodock_vina on all clusters.
Machine Version Module
None Available N/A N/A
▶ **FIX-ME** FAQ?

Usage

AutoDock Vina can use multiple cores in computation by adding --cpu arg .


The usage summary can be obtained with "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 
		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

For convenience, some command line options can be placed into a configuration file.
e.g.
    receptor = hsg1/rigid.pdbqt
    ligand = ligand.pdbqt
    center_x =  2
    center_y =  6
    center_z = -7
    size_x = 25
    size_y = 25
    size_z = 25
    energy_range = 4

Resources

Last modified: April 04 2016 15:23:17.