ABINIT for free energy calculations
DL_POLY
Making it rain: Cloud-based molecular simulations for everyone
There is a recent paper that covers this topic by Lin and MacKerell 1, Force fields for small molecules.
OPLS-All-Atom (OPLS-AA)
OPLS3
CHARMM General force field (CGenFF) see ParamChem
General AMBER Force Field (GAFF)
Merck Molecular Force Field (MMFF)
GROMOS
Drude Polarizable Force Field for Small Organic Molecules
Drude General Force Field (DGenFF)
Parameters for drug-like small molecules have not been reported with the AMBER polarizable force field or CHARMM FQ models.
To validate the parameters:
Force Field Toolkit (ffTK)
General Automatic Atomic Model Parametrization (GAAMP) utility
Also see the MacKerrell lab website
kaggle notebook on kinase inhibitors
Tutorial - Quantum Chemistry with Gaussian using GaussView
Explore using treeClust (machine learning) to uncover associations between residues that have high RMSD => allostery
Lin, F.Y., and MacKerell, A.D. (2019). Force Fields for Small Molecules. Methods Mol. Biol. 2022: 21–54. doi: 10.1007/978-1-4939-9608-7_2 ↩︎