ABS:Mm gff

Molecular Mechanics

• Atom based: atoms are the basic particles; electron and nuclei information are averaged out
• Classical: atoms interact with each other according to classical force field (or potential energy function)
• Additive: the total energy (Hamiltonian) is a sum of all pair-wise interactions
• Empirical: can be parameterized from ab initio calculations or experimental data
  

$x^{2}$

$U=U_{bonded}+U_{nonbonded}\,$ $\sum _{a}^{b}x_{c}$

Intermolecular (nonbonded) force

An excellent mongraph by Stone

• Long range: U ~ R-n
  • Electrostatic (permanent charges, dipoles and quadrupoles…) +/-
  • Induction: Permanent and induced -
  • Instantaneous induction: dispersion -
  • Resonance and magnetic +/-
• Short range: U~ exp(-cR)
  • Exchange -
  • Repulsion +
  • Charge transfer -
  • Penetration -
  • Damping +
    

A quantitative comparison:

General force fields

• MMx (Allinger)
• AMBER
• CHARMM
• OPLSAA
• GROMOS
• AMOBEA

Software and Documentation

Public MM software with manuals that describe force fields:

• AMBER
• GROMACS
• NAMD
• DL Poly manual: http://www.cse.scitech.ac.uk/ccg/software/DL_POLY/MANUALS/USRMAN3.09.pdf or http://wanglab.bu.edu/DLPOLY2/node82.html
• Moldy manual: ftp://ftp.dl.ac.uk/ccp5/MOLDY/moldy.pdf
• MSI manual is another good source

Reviews

Ponder and Case 2003

Mackerrel 2004

Cieplak 2009

Most developments in the polarizable force fields for biomolecules
relate to explicitly induced dipoles and somewhat less to
fluctuating charge and Drude oscillator methods. New
methods have begun to emerge, such as those that go
beyond point charge models and describe charge densities
via spatial functions.