vtlim / Hv1

Free energy perturbation calculations for Hv1 protein

Hv1

This repository was created to house scripts related to molecular dynamics simulations on the Hv1 protein. The subdirectories were numbered to maintain file organization across multiple clusters but not all subdirectories have scripts here. Other components were complex enough to warrant their own repositories, which are hyperlinked. The most relevant and up-to-date preparation and analysis scripts in this repo are those for FEP calculations.

1. Docking
2. Pose analysis
3. Ligand in water box - no scripts
4. FEP
5. QM dihedral scan - see this repo
6. QM tautomers - no scripts
7. MM dihedral scan - umbrella sampling, for extraBonds restraints see #5.
8. Permeation - see this repo
9. REST2