Documentation2019-04-25T23:43:32+00:00

This page was last updated on April 25th, 2019 at 11:43 pm

AutoGridFR documentation

AutoGridFR (or AGFR in short) is a software program facilitating the calculation of AutoDock4 affinity maps. It is usable from the command line of through Graphical User Interface (GUI).

In this quick overview we highlight the main components of the GUI and the general workflow for preparing a target file. More detailed tutorials on using the GUI for various scenarios are available below. Examples of using the command line interface are available in the tutorials for docking with ADFR.

Step-by-step tutorials

Prerequisites

run ADFRsuite-1.0/bin/agfrgui to start the Graphical User interface for these tutorials.

FAQ

How can I inspect a target file2019-04-15T20:03:03+00:00

Target files can be inspected visually using AutoDockSuite-$VERSION/bin/agfrgui. Alternatively AutoDockSuite-$VERSION/bin/about can be used to display the meta-data associate with a target file as shown below.

> about NativeCDK2BindingSite_rigid.trg
docking target file
date : Mon Jan 28 18:54:17 2019
node : fiji
platform : Darwin-17.7.0-x86_64-i386-64bit

receptor : 4EK3_rec.pdbqt
FlexRec : None
covBond : No

box : 
center : 23.332 28.922 29.598
length : 17.250 16.500 12.000
size : 0046 0044 0032
spacing : 0.375

maps : C A e d OA Br NA HD N W 
pocketMode : ['user', 23.332000000000001, 28.922000000000001, 29.597999999999999, 17.25, 16.5, 12.0]
#fillpts : 247 points
file : NativeCDK2BindingSite_rigid/translationPoints.npy
>