How to install MolKit for flexible docking using script prepare_flexreceptor.py?

[emilyrkang]

I'm following the Flexible Docking tutorial found here: https://autodock-vina.readthedocs.io/en/latest/docking_flexible.html on an AWS ubuntu instance.

When I try to run the prepare_flexreceptor.py script I get an import error. However, I can't install the module with pip or sudo apt install. I downloaded and installed the Linux GUI installer from here: https://ccsb.scripps.edu/mgltools/downloads/ but I'm still getting the error. How can I install this module? Else is there a way to use AutoDock Vina with flexible side chains without it?

Traceback (most recent call last):
  File "prepare_flexreceptor.py", line 9, in <module>
    from MolKit import Read
ImportError: No module named MolKit
(vina) ubuntu@myip:~/ERK/adv_py_test$ pip install MolKit
ERROR: Could not find a version that satisfies the requirement MolKit (from versions: none)
ERROR: No matching distribution found for MolKit
(vina) ubuntu@myip:~/ERK/adv_py_test$

./mgltools_Linux-x86_64_1.5.7_install

This will install mgltools on your computer.  Continue? [n/Y] Y

Where do you want to install mgltools? [/home/ubuntu/MGLTools-1.5.7]

Installing mgltools...                                                        Installing Program Files...
Installation complete.

$ sudo apt install mgltools-molkit
Reading package lists... Done
Building dependency tree
Reading state information... Done
E: Unable to locate package mgltools-molkit

[gjonwick]

Did you try to set up your environment for command line usage? If not, try following the instructions in the README file that comes with MGLTools.

[diogomart]

Currently, the only way to prepare flexible sidechains is with MGLTools. We don't have an alternative yet. MGLTools comes with an installer, which is probably the only way to install it properly, and has it's own python version, which is called from a shell script named pythonsh. The scripts are meant to be run using this pythonsh.