The README File

An Informal AMBER Small Molecule Force Field: parm@Frosst

Credit
Christopher Bayly, lead the effort between (1992-2010)
Daniel McKay, contributed between (1997-2010)
Jean-Fran├žois Truchon, contributed between (2002-2010)

This presents a molecular mechanics force field (FF) extending the AMBER FF to bioorganic small molecules of pharmaceutical interest. The presented parm@Frosst FF enables the simulation of biomolecules (enzymes, DNA, peptides, etc.) in the presence of complex organic molecules such as inhibitor and cofactors. As such it can be used as a small-molecule supplement to the AMBER parm9x or ffxx biomolecular force fields, as an alternative to e.g. gaff. The development took place at Merck Frosst Canada, a subsidiary of Merck & Co, between 1992 and 2010 in the context of numerous drug-discovery projects. As a result, parm@Frosst, when used to extend one of the "standard" AMBER force fields such as ff99sb, could successfully parameterize approximately 85% of the Merck corporate collection (of small molecules) in 2009 (personal communication to CIB from V. Hornak). Merck & Co generously cleared this material to be released to the scientific community. John Irwin and Brian Schoichet generously permitted us to use a fraction of the ZINC dataset (zinc.docking.org). This data repository contains enough information to 1) implement the parm@Frosst force field and validate the implementation 2) validate the atom and bond typing of an implementation of the AM1BCC charge model as originally published.

File List for parm_at_Frosst Directory

You can also retrieve all the files listed above as a compressed tar (parm_at_Frosst.tgz) or a zip (parm_at_Frosst.zip) archive.

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