parameterize is a tool to obtain force field parameters for new molecules easily and efficiently.
Commonly used AMBER and CHARMM force fields contain parameters for biomolecules (proteins, nucleotides, saccharides, lipids, etc.), but lack parameters for other biologically relevant molecules (co-factors, drugs, etc.).
GAFF and CGenFF address this by using empirical rules and pre-computed data sets to derive parameters for arbitrary organic molecules. However, these parameters are not guaranteed to be transferable to all possible chemical environments.
parameterize improves the quality of the parameters by using QM data, i.e. refitting ESP charges and rotatable
dihedral angle parameters. It fundamentally solves the problem of transferability.
GAFF and GAFF2 (for AMBER)
CGenFF (for CHARMM)
Fitted to reproduce the electrostatic potential (ESP) of QM
Selected charges can be fixed during the fitting
Automatic rotatable dihedral detection
Automatic identical dihedral detection
Dihedral scanning with and without QM structure optimization
Parameter fitting to reproduce QM energies
LSF/Slurm queuing systems
parameterize comes with HTMD. It takes a MOL2 file, parameterizes it, and outputs force field files in CHARMM and
AMBER formats. There are many options that are shown in detail below. The structure inside the output directory
(controlled by the
--output flag) is the following:
. ├── dihedral-opt ├── esp ├── minimize └── parameters
The output inside
minimize/ is related with the QM calculations performed during
the parameterization of the molecule and work as check-points for the different steps of the parameterization process.
parameters is where the relevant outputs are written with following format:
parameters/<force-field>/<theory>-<basis-set>-<vacuum/water>/. Inside this directory there are the force-field
parameter files, as well as a
plots/ directory, where one can check the optimization carried on by the tool.