An Informal AMBER Small Molecule Force Field:
Christopher Bayly, lead the effort between (1992-2010)
Daniel McKay, contributed between (1997-2010)
Jean-François 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.
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.NOTE THAT E-MAIL ADDRESSES HAVE BEEN MODIFIED!!!