Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing

By Kenno Vanommeslaeghe, Alexander D. MacKerell. Journal of Chemical Information and Modeling, 2012

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From Proteins to Perturbed Hamiltonians: A Suite of Tutorials for the GROMACS-2018 Molecular Simulation Package [Article v1.0] (2019, methodology): “CGenFF is both a parameter set (compatible with the CHARMM force field) and a program that builds smallmolecule topologies according to existing rules [70, 71].”
LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands (2017, background): “For commercial re-use, please contact journals.permissions@oup.com with parameters from the CHARMM36/CGenFF force field and charges assigned by analogy.”
Driven to Near-Experimental Accuracy by Refinement via Molecular Dynamics Simulations (2019, background): “32,33 For metal ions, additional distance restraints were applied to enforce their predicted coordination geometry with conserved nearby amino acids.”
Computer-Aided Drug Design Methods (2017, methodology): “When parameters are missing in the existing force field, which is common for small drug-like molecules, automated parameter generation programs such as the CGenFF program (41, 42) or Antechamber (43) can be used to complete the force field.”
Positive allosteric mechanisms of adenosine A1 receptor-mediated analgesia (2021, methodology): “Force field parameters of the agonist ADO and PAM MIPS521 were obtained from the CHARMM ParamChem web server[64, 65].”