AMDock (Assisted Molecular Docking) is a user-friendly graphical tool to assist in the docking of protein-ligand complexes using Autodock-Vina or AutoDock4. This tool integrates several external programs for processing docking input files, define the search space (box) and perform docking under user’s supervision.
Version 1.5.x for Linux (Build 1.5.0)
DOCUMENTATION
Manual, tutorials and test files are located in Doc folder. (May be out of date. Please check the wiki)
Cite us
Valdes-Tresanco, M.S., Valdes-Tresanco, M.E., Valiente, P.A. and Moreno E. AMDock: a versatile graphical tool for assisting molecular docking with Autodock Vina and Autodock4. Biol Direct 15, 12 (2020). https://doi.org/10.1186/s13062-020-00267-2
INSTALL
-unzip the *.zip file
-execute ./install.sh and follow instructions
If ./install.sh is not running, change the execution permissions. To do this press
right click > permissions > Allow execute this file as a program
Before installation, verify that you have PyMOL, PyQt4 and numpy as python
modules, if not, execute in a terminal
sudo apt install pymol python-qt4 python-numpy openbabel
Before using the program, check that PyMOL has the AMDock plugin in taskbar.
If it does not appear please follow the instructions:
-open PyMOL > Plugins > Manager Plugins > Settings > Add new directory
PyMOL should automatically have:
~/.pymol/startup or /home/user_name/.pymol/startup if not, please select the previous address
after this you must restart PyMol
Automatically, a file (AMDock.desktop) must be generated that allows its execution from the start menu. If you use
a linux version where it doesn't appear, you can run it through the terminal:
installation folder> right click> run a terminal here> (in terminal) ./AMDock.sh
UNINSTALL
Just search the installation directory and execute ./uninstall.sh in a terminal and follow instructions
To view the update history, please check Changes_History file
TUTORIALS
Please, check the wiki https://github.com/Valdes-Tresanco-MS/AMDock-win/wiki
This project is possible thanks to the Open Source license of the JetBrains programs.