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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.

Shells

A user may choose between using /bin/bash and /bin/tcsh. Details about each shell follows.

/bin/bash

System resource file: /etc/profile

When one access the shell, the following user files are read in if they exist (in order):

  1. ~/.bash_profile (anything sent to STDOUT or STDERR will cause things like rsync to break)
  2. ~/.bashrc (interactive login only)
  3. ~/.profile

When a user logs out of an interactive session, the file ~/.bash_logout is executed if it exists.

The default value of the environmental variable, PATH, is set automatically using SoftEnv. See below for more information.

/bin/tcsh

The file ~/.cshrc is used to customize the user's environment if his login shell is /bin/tcsh.

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

The command softenv will provide a list of available packages. The listing will look something like:

$ 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
... some stuff deleted ...
Managing 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

The command soft can be used to manipulate the environment from the command line. It takes the form:

$ soft add/delete +keyword

Using this method of adding or removing keywords requires the user to pay attention to possible order dependencies. That is, best results require the user to remove keywords in the reverse order in which they were added. It is handy to test out individual keys, but can lead to trouble if changing multiple keys. Changing the .soft file and issuing the resoft is the recommended way of dealing with multiple changes.

▶ Display Module Names for autodock_vina on all clusters.
Machine Version Module
None Available N/A N/A
▶ Module FAQ?

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

Shells

A user may choose between using /bin/bash and /bin/tcsh. Details about each shell follows.

/bin/bash

System resource file: /etc/profile

When one access the shell, the following user files are read in if they exist (in order):

  1. ~/.bash_profile (anything sent to STDOUT or STDERR will cause things like rsync to break)
  2. ~/.bashrc (interactive login only)
  3. ~/.profile

When a user logs out of an interactive session, the file ~/.bash_logout is executed if it exists.

The default value of the environmental variable, PATH, is set automatically using SoftEnv. See below for more information.

/bin/tcsh

The file ~/.cshrc is used to customize the user's environment if his login shell is /bin/tcsh.

Modules

Modules is a utility which helps users manage the complex business of setting up their shell environment in the face of potentially conflicting application versions and libraries.

Default Setup

When a user logs in, the system looks for a file named .modules in their home directory. This file contains module commands to set up the initial shell environment.

Viewing Available Modules

The command

$ module avail

displays a list of all the modules available. The list will look something like:

--- some stuff deleted ---
velvet/1.2.10/INTEL-14.0.2
vmatch/2.2.2

---------------- /usr/local/packages/Modules/modulefiles/admin -----------------
EasyBuild/1.11.1       GCC/4.9.0              INTEL-140-MPICH/3.1.1
EasyBuild/1.13.0       INTEL/14.0.2           INTEL-140-MVAPICH2/2.0
--- some stuff deleted ---

The module names take the form appname/version/compiler, providing the application name, the version, and information about how it was compiled (if needed).

Managing Modules

Besides avail, there are other basic module commands to use for manipulating the environment. These include:

add/load mod1 mod2 ... modn . . . Add modules
rm/unload mod1 mod2 ... modn  . . Remove modules
switch/swap mod . . . . . . . . . Switch or swap one module for another
display/show  . . . . . . . . . . List modules loaded in the environment
avail . . . . . . . . . . . . . . List available module names
whatis mod1 mod2 ... modn . . . . Describe listed modules

The -h option to module will list all available commands.

Module is currently available only on SuperMIC.

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.