1. Charmm-GUI https://www.charmm-gui.org/ （namd and genesis for ligand binding and mutation）
genesis ： https://www.r-ccs.riken.jp/labs/cbrt/
2. Galaxy CompChem ZA https://galaxy-compchem.ilifu.ac.za/ （gromacs for ligand binding）
3. BioExcel Building Blocks http://mmb.irbbarcelona.org/biobb/
4. pmx http://pmx.mpibpc.mpg.de/webserver.html （https://github.com/deGrootLab/pmx/）（gromacs for mutation）
5. BFEE2 https://pypi.org/project/BFEE2/ (https://github.com/fhh2626/BFEE2) For WTM-eABF (well-tempered metadynamics-extended adaptive biasing force 扩展自适应偏置力)
MULE https://github.com/fhh2626/Multidimensional-lowest-energy--Mule 使用MULE在势能面/自由能面上寻找最低反应路径
6. PyAutoFEP https://github.com/luancarvalhomartins/PyAutoFEP
PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methodsPyAutoFEP is a tool to automate Free Energy Perturbations (FEP) calculations to estimate Relative Free Energies of Binding (RFEB) of small molecules to macromolecular targets. It automates the generation of perturbation maps, the building of dual-topologies for ligand pairs, the setup of MD systems, and the analysis. Distinctivelly, PyAutoFEP supports multiple force fields, integrates enhanced sampling methods, and allows flexible λ windows schemes. Furthermore, it aims to be as flexible as possible, giving the user great control over all steps. Nevertheless, reasonable defaults and automation are provided, so that PyAutoFEP can be used by non experts. PyAutoFEP is written in Python3 and uses GROMACS.
7. ProtoCaller https://github.com/protocaller/protocaller
Full automation of relative protein-ligand binding free energy calculations in GROMACS with BAR
8. BAT.py for Amber (absolute binding free energy) https://github.com/GHeinzelmann/BAT.py
The Binding Affinity Tool (BAT.py) is a python tool for fully automated absolute binding free energy calculations. Its workflow encompasses the creation of the bound complex, generation of parameters using Antechamber, preparation of the simulation files, and post-processing to retrieve the binding free energy. By using the pmemd.cuda software from AMBER20, it is able to perform several calculations at a reduced computational cost using graphics processing units (GPUs). The 2.0 version of BAT.py can perform binding free energy calculations by two alchemical routes in the presence of restraints, either with double decoupling (DD) procedure or with the simultaneous decoupling recoupling (SDR) method. For the use of the APR method in addition to DD and SDR, download the 1.0 version of the code at the BATv1.0 branch. BAT.py is compatible with the simulation package AMBER20, also requiring a few installed programs to work properly, which are listed in the next section.
9. Perturbation Free-Energy Toolkit: An Automated Alchemical Topology Builder
This toolkit is aimed at facilitating setup and analysis of MD simulations, e.g. perturbation free energy calculations.
10. seekr2 https://seekr2.readthedocs.io/en/latest/installation.html
SEEKR2: Multiscale Milestoning Calculations of Kinetics and Thermodynamics