This project contains scripts to automate preparing of ligand gated ion channels.


It consists of the following tools

createProject.py
membed.py
prepare.py
run_ems.py
run_equis.py


createProject.py
==================
creates a project structure this is the first script to use


membed.py
==================
embeds a protein into a membrane
This one takes a while to run and uses g_membed
After this step you will have a proper topology and structure to simulate

NOTE: after this step you might want to run a manual grompp and make sure everything looks alright

prepare.py
===================
If multiple conformation of the same structure is needed use this script.
It takes the given structures and applies the membrane generated in membed.py.
this one does not do g_membed but simply concatenates the protein structure with the non protein molecules
of the structure created by membed.py.
it also assumes that the topology generated from membed.py is reusable


ensemble.py
==============
 given starting structures this script can protonate and mutate each structure and prepare topologies


run_cpc
===================
creates a copernicus workflow and submits all the structures in the confs folder to it
requires mdp files to be provided separately

can create an em and a production workflow