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-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.

File List for parm_at_Frosst Directory

• parm_Frosst_note.pdf [321kB] : Note about the history and the content of the parm@Frosst FF.
  
• mmff94_am1bcc_atypes.txt [101kB] : The MMFF94 set AM1-BCC atom types. One type per line. This exactly matches the atom ordering found in the mmff94.sdf file.
  
• mmff94_am1bcc_btypes.txt [35kB] : The MMFF94 set AM1-BCC bond types. One type per line. This exactly matches the bond list found in mmff94.sdf file.
  
• parm_Frosst.frcmod [151kB] : The AMBER FF parameters specific to small bioorganic.
  
• parm_Frosst.pcp [6kB] : The typing rules in PATTY format.
  
• zinc.sdf [20500kB] : ZINC set: three dimensional structures in the MDL SD format from a subset of the ZINC dataset.
  
• zinc_p_f_types.txt [622kB] : The ZINC set parm@Frosst atom types. One type per line. This exactly matches the atom ordering found in the zinc.sdf file.
  
• zinc_am1bcc_atypes.txt [1275kB] : The ZINC set AM1-BCC atom types. One type per line. This exactly matches the atom ordering found in the zinc.sdf file.
  
• zinc_am1bcc_btypes.txt [449kB] : The ZINC set AM1-BCC bond types. One type per line. This exactly matches the bond list found in the zinc.sdf file.
  
• mmff94.sdf [1628kB] : MMFF94 validation : three dimensional structures in the MDL SD format.
  
• mmff94_p_f_types.txt [48kB] : The parm@Frosst atom types of MMFF94 set. One type per line. This exactly match the atom ordering found in the mmff94.sdf file.