SIMONAPreprocessor
Forcefields used by SIMONA

Forcefields for POEM++ and Generic Monte Carlo

Lennard Jones
The van der Waals interactions are included as Lennard-Jones 6-12 potential.
  • Lennard Jones
  • PFF - Lennard Jones
  • PFF - Clash Potential
  • PFF - Rigid body LJ
  • AMBER - 6,12-Lennard-Jones
  • AMBER - 6,12-Lennard-Jones for 1,4-neighbours
Electrostatics
The electrostatics is included using Coulomb potential.
  • PFF - Electrostatics
  • PFF - HBonds
  • Coulomb electrostatics (all-atom)
  • AMBER Coulomb electrostatics (with exclude list)
  • AMBER Coulomb electrostatics for 1,4-neighbours
Implicit Solvent
  • PFF - Implicit solvent energy
  • PFF - PowerSasa
  • Non-polar solvation energy
  • ALPB Still
  • Born radii
Constraint Potentials
  • PFF - Rama
  • DFire
  • Amber dihedral potential
  • Gaussian network model
Interface Potentials
  • IO Interface Potential
Additional Potentials
  • Pit Potentials
  • Z-driving Potential
Membrane Potentials
  • Membrane Implicit Solvent Energy
PFF01 (Protein Force Field 01)
The PFF01 forcefield contains the following forcefield terms:
  • PFF - Clash
  • PFF - LennardJones
  • PFF - HBond
  • PFF - Electrostatics without elocal (local electrostatics)
  • PFF - PowerSASA
  • PFF - ImplicitSolventEnergy
PFF02 (Protein Force Field 02)
The PFF02 forcefield contains the following forcefield terms:
  • PFF - Clash
  • PFF - LennardJones
  • PFF - HBond
  • PFF - Electrostatics with elocal (local electrostatics)
  • PFF - PowerSASA
  • PFF - ImplicitSolventEnergy
  • PFF - Rama


Forcefields for FlexScreen

  • FlexScreen Lennard Jones
  • FlexScreen HBonds
  • FlexScreen Electrostatics
  • FlexScreen Implicit Solvent Energy
  • FlexScreen Lennnard Jones + HBond Grid
  • FlexScreen Electrostatic Grid
    Todo:
    explanation of forcefields