Potential Examples
Available Force Fields
Force Field X stores AMOEBA force fields internally. The 2009 AMOEBA Biomolecular force field is specified as:
The following force fields may also be specified. Except where noted, they have been imported from the TINKER v. 5.1 distribution.
forcefield amoeba-bio-2009
- amoeba-water the 2003 Ren and Ponder AMOEBA water model (water.prm)
- amoeba-2004 initial AMOEBA small molecule parameters (amoeba04.prm)
- amoeba-2009 2009 update to the AMOEBA small molecule parameters (amoeba09.prm)
- amoeba-protein-2004 initial AMOEBA protein force field (amoebapro04.prm)
- amoeba-protein-2004-u1 an update to the initial AMOEBA protein force field based on validation stuides done in the Ren lab
- amoeba-bio-2009 the 2009 update to the AMOEBA protein force field and initial AMOEBA nucleic acid force field (amoebabio09.prm)
DHFR Example
Force Field X reproduces TINKER v. 5.1 potential energy values to more than 10 significant digits on large, solvated systems. For example, our test suite includes the classic DHFR bench mark as well as solvated ubiquitin.
The DHFR property file:
Force Field X output from the "energy" script command on DHFR:
The TINKER v. 5.1 analyze output for DHFR:
Computed Potential Energy
Bond Streching 6423.84579926 16569
Angle Bending 3746.31506290 11584
Stretch-Bend -21.85553039 4031
Urey-Bradley 687.46861123 7023
Out-of-Plane Bend 198.72886589 1566
Torsional Angle 426.23738971 6701
Pi-Orbital Torsion 48.26628393 292
Torsion-Torsion -41.71473465 147
Van der Waals 32646.72296810 3480445
Atomic Multipoles -79415.53874329 1463353
Polarization -32001.56811430 1463353
Total Potential -67303.09214161 (Kcal/mole)
forcefield amoeba-bio-2009
a-axis 62.23
b-axis 62.23
c-axis 62.23
alpha 90.00
beta 90.00
gamma 90.00
spacegroup P1
vdw-cutoff 9.00
ewald-cutoff 6.70
ewald-alpha 0.57
pme-order 5
polar-eps 0.01
pme-spacing 1.00
Total Potential Energy : -67303.09214149 Kcal/mole
Energy Component Breakdown : Kcal/mole Interactions
Bond Stretching 6423.84579926 16569
Angle Bending 3746.31506290 11584
Stretch-Bend -21.85553039 4031
Urey-Bradley 687.46861123 7023
Out-of-Plane Bend 198.72886589 1566
Torsional Angle 426.23738971 6701
Pi-Orbital Torsion 48.26628393 292
Torsion-Torsion -41.71473465 147
Van der Waals 32646.72296821 3480445
Atomic Multipoles -79415.53874328 1463353
Polarization -32001.56811430 1463353
Ubiquitin Example
The Ubituitin property file:
Force Field X output from the "energy" script command on Ubiquitin:
The TINKER v. 5.1 analyze output for Ubiquitin:
Computed Potential Energy
Bond Streching 2673.37683484 6908
Angle Bending 1637.34919041 5094
Stretch-Bend -11.04350364 1958
Urey-Bradley 279.64162198 2835
Out-of-Plane Bend 67.64798284 651
Torsional Angle 215.14214012 3297
Pi-Orbital Torsion 24.69060350 106
Torsion-Torsion -29.43681349 71
Van der Waals 13202.86995844 1483768
Atomic Multipoles -33012.66179952 623490
Polarization -12918.82414755 623490
Total Potential -27871.24793207 (Kcal/mole)
parameters amoeba-bio-2009
a-axis 54.99
b-axis 41.91
c-axis 41.91
spacegroup P1
vdw-cutoff 9.00
ewald-cutoff 6.70
ewald-alpha 0.57
pme-order 5
polar-eps 0.01
Total Potential Energy : -27871.24793201 Kcal/mole
Energy Component Breakdown : Kcal/mole Interactions
Bond Stretching 2673.37683484 6908
Angle Bending 1637.34919041 5094
Stretch-Bend -11.04350364 1958
Urey-Bradley 279.64162198 2835
Out-of-Plane Bend 67.64798284 651
Torsional Angle 215.14214012 3297
Pi-Orbital Torsion 24.69060350 106
Torsion-Torsion -29.43681349 71
Van der Waals 13202.86995849 1483768
Atomic Multipoles -33012.66179952 623490
Polarization -12918.82414755 623490