GAFF2 Molecule

The GAFF2 Molecule follows similar paradigms as the CGenFF Molecule in terms of parsing. GAFF2 also includes a penalty score which makes this more interesting to capture.

The equation differs slightly in terms of the harmonics and recent additions have been the impropers. The parser was built to handle frcmod files into dataframes and update their values accordingly.

An example of the format can be found here in terms of how the frcmod is defined and what all the numbers mean:

BOND
atom type | force constant | bond length
ca-ns  315.20   1.412       same as ca- n, penalty score=  0.0

ANGLE
atom type | force constant | angle degree
c -ns-ca   65.700     123.710   same as c -n -ca, penalty score=  0.0

DIHE
atom type | idivf1 | force constant | phase | periodicity
o -c -ns-ca   4   10.000       180.000           2.000      same as X -c -n -X , penalty score=  0.0

IMPROPER
atom type | force constant | phase | periodicity
ca-ca-ca-ns         1.1          180.0         2.0          Using the default value

NONBON
atom type | rmin half | epsilon

Import the Package

from global_chem_extensions import GlobalChemExtensions
gce = GlobalChemExtensions()

Read in GAFF2 frcmod File

Code

gaff2_molecule = gce.initialize_gaff2_molecule('file.frcmod')
print (gaff2_molecule)

Access Non-Bonded and Bonded DataFrames

Code

gaff2_molecule = gce.initialize_gaff2_molecule('file.frcmod')
print (gaff2_molecule.nonbonded_dataframe)
print (gaff2_molecule.bonded_dataframe)

Update a value in Bonded DataFrames

Harmonic values refers to anything that is either a bond-length, angle, dihedral or improper angle. Multiplicity only refers to dihedrals or impropers.

Code

gaff2_molecule = gce.initialize_gaff2_molecule('file.frcmod')

gaff2_molecule.update_bonded_dataframe(
    'ca-ca-ns-hn',
     200,
     force_constant=True,
     harmonic_value=False,
     multiplicity=False,
     fluctuation=False,
     )

print (gaff2_molecule.new_bonded_dataframe)

Access Manipulated Non-Bonded and Bonded DataFrames

The values to update are the Rmin and the epsilon values.

Code

gaff2_molecule = gce.initialize_gaff2_molecule('file.frcmod')

gaff2_molecule.update_nonbonded_dataframe(
'ca-ca',
 3,
 rmin=True,
 epsilon=False,
 )
print (gaff2_molecule.new_nonbonded_dataframe)

Write a new Frcmod GAFF2 File

Code

gaff2_molecule = gce.initialize_gaff2_molecule('file.frcmod')
cgenff_molecule.write_frcmod_file()

Output

Remark line goes here
MASS
BONDS
ca-ns	1.412	315.20
c-ns	1.379	356.20
hn-ns	1.013	527.30

ANGLE
c-ns-ca	123.710	65.700
ca-ns-hn	116.000	48.000
ns-c-o	123.050	113.800
c-ns-hn	117.550	48.700
ca-ca-ns	120.190	85.600
c3-c-ns	115.180	84.300

DIHE
o-c-ns-ca	4	10.000	180.000	2.000
c3-c-ns-ca	1	0.750	180.000	-2.000
c3-c-ns-ca	1	0.500	0.000	3.000
o-c-ns-hn	1	2.500	180.000	-2.000
o-c-ns-hn	1	2.000	0.000	1.000
ca-ca-ns-c	1	0.950	180.000	2.000
ns-c-c3-c3	1	0.000	180.000	-4.000
ns-c-c3-c3	1	0.710	180.000	2.000
ca-ca-ns-hn	4	1.800	180.000	2.000
c3-c-ns-hn	4	10.000	180.000	2.000

IMPROPER
ca-ca-ca-ns-1.1	180.0	2.0 
ca-ca-ca-ha-1.1	180.0	2.0 
c3-ns-c-o-10.5	180.0	2.0 
c-ca-ns-hn-1.1	180.0	2.0 
ca-h4-ca-nb-1.1	180.0	2.0 


NONBON
ca-h4	1.1	180.0
ca-h4	1.1	180.0

Accessing Properties on GAFF2 Molecule

print (gaff2_molecule.bond_parameters)
print (gaff2_molecule.angle_parameters)
print (gaff2_molecule.dihedral_parameters)
print (gaff2_molecule.nonbonded_parameters)
print (gaff2_molecule.improper_parameters)