Method

A method implemented in parameterize is inspired by GAAMP [1]. A detailed description of our method will be published soon [2].

General procedure

  1. Get initial parameters (from GAFF or CGenFF)
  2. Minimize the geometry of molecule with QM
  3. Get atomic charges:
    1. Compute ESP with QM
    2. Fit the atomic charges to reproduce the QM results
  4. Get dihedral angle parameters:
    1. Detect rotatable dihedral angles
    2. Scan the dihedral angles with QM
    3. Fit the parameters to reproduce the QM results
  5. Check parameterization quality:
    1. Plot rotamer QM and MM energies
[1]L. Huang and B. Roux, Automated Force Field Parameterization for Nonpolarizable and Polarizable Atomic Models Based on Ab Initio Target Data, J. Chem. Theory Comput., 2013, 9 (8), pp 3543–3556. doi: 10.1021/ct4003477
[2]M. J. Harvey, J. M. Damas, G. Martínez and G. De Fabritiis, Small Molecule Forcefield Parameterization with HTMD, in preparation.