amberff

These module files provide parameter sets for the popular Amber force fields as Python modules. See the original references, linked below, for an explanation of these paramters.

How to use these modules

Quickstart

Import the module into your code.

>>> import gaffparams

>>> mycarbon = gaffparams.Atoms['c']
>>> mycarbon.mass
12.01
>>> mycarbon.comment
'Sp2 C carbonyl group'

>>> c_ca_bond = gaffparams.Bonds['c-ca']
>>> c_ca_bond.k
349.7
>>> c_ca_bond.r0
1.487
>>> c_ca_bond.comment
'SOURCE1     480\t0.0055'

Torsion parameters sometimes have multiple terms, so a list of the Torsion objects are returned.

>>> tor = gaffparams.Torsions['hc-c3-c3-c']
>>> for term in tor:
...     print term.bondpaths,term.Vn2,term.gamma
...
1 0.16 0.0
1 0.0 0.0
1 0.25 0.0

Attributes

• Atoms: mass, comment
• Bonds: k, r0, comment
• Angle: k, theta0, comment
• Torsion: bondpaths, Vn2, gamma, period, comment
• Improper: Vn2, gamma, period, comment
• Vdw: R, epsilon, comment

More Information

Each module contains several dictionaries:

• Atoms
• Bonds
• Torsions
• Impropers
• VdWs

The dictionary keys correspond to the identifiers used in the reference paramter files. This amounts to the atom type, or the hyphen-separated atom types for angles and torsions. Spaces are removed.

Here are a few lines from parm94.dat, for example:

BR 79.90                !            bromine
C  12.01                             sp2 C carbonyl group
...
C -CA  469.0    1.409       JCC,7,(1986),230; TYR
C -CB  447.0    1.419       JCC,7,(1986),230; GUA
...
CB-C -NA    70.0      111.30    NA
CB-C -O     80.0      128.80
...
X -C -CA-X    4   14.50        180.0             2.         intrpol.bsd.on C6H6
X -C -CB-X    4   12.00        180.0             2.         intrpol.bsd.on C6H6

Each value in the dictionary is a namedtuple with fields for each type of parameter associated with the entity.

• Atoms: mass, comment
• Bonds: k, r0, comment
• Angle: k, theta0, comment
• Torsion: bondpaths, Vn2, gamma, period, comment
• Improper: Vn2, gamma, period, comment
• Vdw: R, epsilon, comment

AMBER94

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules http://ffamber.cnsm.csulb.edu/pdfs/cornell_amber94_1995jacs.pdf

Amber 94 not currently included

GAFF

Development and Testing of a General Amber Force Field http://ambermd.org/antechamber/gaff.pdf

About Amber parameters and units

Atoms

• Mass of atoms (mass) is recorded in Atomic Mass Units

Bonds

• The bond stretch force constant (k) is stored in kcal/(mol * A^2)
• The idealized bond length (r0) is in Angstroms

Angles

• The angle force constant (k) is stored in kcal/(mol * radian^2)
• The idealized angle (theta0) is stored in degrees

Torsions

• The torsion bond path (bondpaths) parameter is the number of bond paths that the total Vn/2 is dividied into. This is equal to the product of the number of bonds leading into the middle two atoms. For example, since X-C-CA-X has 4 bond paths, each of them has a Vn/2 of 14.5/4 kcal/mol assigned to it

• The magnitude of the torsion, Vn/2 (stored as Vn2) is in kcal/mol

• (gamma) is the ideal phase offset of the torsion in degrees

• (period) is the periodicity of the torsion

VdW

• (R) is the Van der Waals radius for the given atom in Angstroms. The value used in eq 1 for an interaction of atom i and atom j is Rij* = Ri* + Rj*

• Epsilon (epsilon) is the Van der Waals well depth in kcal/mol