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.