xparamber1:
AMBER parametrization automation
Script that automates the process of parameterizing small ligand molecules in th e AMBER forcefield using the AmberTools package.
walkermaker:
Tools for generating walkers
These tools help with generating multiple starting positions for a ligand to be used in a metadynamics simulation.
restminimizer:
Scripts for running em with restrains
The ndxmaker.sh program generates an .ndx file, which is then used to create a . posre file.
The runrestrained_em.sh program performs energy minimization for multiple walker s using a .posre file.
reboxing
Move your walkers into new box
fixpbc.sh - repair Ligand destroyed by PBC
solver.sh - Change the type and size of box, and then solvate system
ionizer.sh - Neutralize system with K and CL ions