The README File
The README File
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
Merck & Co generously cleared this material to be released to the
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
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
- 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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