parm_at_Frosst
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The README File

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

  • 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.

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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