https://github.com/vtlim/hv1

Free energy perturbation calculations for Hv1 protein
https://github.com/vtlim/hv1

Last synced: about 1 month ago
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Free energy perturbation calculations for Hv1 protein

• Host: GitHub
• URL: https://github.com/vtlim/hv1
• Owner: vtlim
• License: mit
• Created: 2016-10-14T05:28:40.000Z (about 8 years ago)
• Default Branch: master
• Last Pushed: 2020-01-23T01:07:02.000Z (almost 5 years ago)
• Last Synced: 2024-10-17T05:33:21.189Z (2 months ago)
• Language: Tcl
• Homepage: https://www.nature.com/articles/s41598-020-70369-4
• Size: 7.36 MB
• Stars: 0
• Watchers: 1
• Forks: 1
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        

# 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](https://github.com/vtlim/dihedral-scan)

6. **QM tautomers** - no scripts

7. **MM dihedral scan** - umbrella sampling, for `extraBonds` restraints see #5.

8. **Permeation** - see this [repo](https://github.com/vtlim/permeability)

9. **REST2**