Different well-established force field sets are handled by the PyRED program:

Use the 'FFPARM' keyword in the 'System.config' configuration file to automatically handle force field atom typing:

KEYWORD	DESCRIPTION
GLYCAMFF04	Glycam04 from the Amber10 distribution
	Kirschner & Woods, Proc.Natl.Acad.Sci.USA 2001 98, 10541.
	Basma et al. J.Comput.Chem. 2001 22, 1125.
	Kirschner & Woods, J.Phys.Chem.A 2001 105, 4150.
Application	Cezard et al. Phys.Chem.Chem.Phys. 2011, 13, 15103.
AMBERFF94	Cornell et al. J.Am.Chem.Soc. 1995 117, 5179.
AMBERFF96	Cornell et al. J.Am.Chem.Soc. 1995 117, 5179.
	Kollman et al. Computer Simulation of Biomolecular Systems,
	ed. Wilkinson, Weiner & van Gunsteren, Elsevier, Escom,
	The Netherlands, 1997 3, 83-96.
AMBERFF98	Cornell et al. J.Am.Chem.Soc. 1995 117, 5179.
	Cheatham et al. J.Biomol.Struct.Dyn. 1999 16, 845.
AMBERFF99	Cornell et al. J.Am.Chem.Soc. 1995 117, 5179.
	Wang et al. J.Comput.Chem. 2000 21, 1049.
AMBERFF99SB	Wang et al. J.Comput.Chem. 2000 21, 1049.
	Hornak et al. Proteins 2006 65, 712.
AMBERFF99SBBSC	Wang et al. J.Comput.Chem. 2000 21, 1049.
	Hornak et al. Proteins 2006 65, 712.
	Perez et al. Biophys.J. 2007 92, 3817.
AMBERFF03	Wang et al. J.Comput.Chem. 2000 21, 1049.
	Duan et al. J.Comput.Chem. 2003 24, 1999.
AMBERFF10	Wang et al. J.Comput.Chem. 2000 21, 1049.
	Hornak et al. Proteins 2006 65, 712.
	Perez et al. Biophys.J. 2007 92, 3817.
	Banas et al. J.Chem.TheoryComput. 2010 6, 3836.
	Zgarbova et al. J.Chem.TheoryComput. 2011 7, 2886.
OFF	No force field atom type is generated

To handle more recent force fields, or to create a new force field:

Use the 'MOLECULE'n'-ATMTYPE' keywords ('n' molecule input number) in the 'Project.config' configuration file to affect force field atom typing.
See also the tutorials below:
Use of the GAFF or GAFF2 and the AmberFF14SB or AmberFF19SB force fields
Generation of a Glycam 2006 or OPLS type force field

Last update of this page: November 30th, 2024.

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