The Force Field Toolkit is comprised of a set of tools that aid users in the development of CHARMM-compatible forcefield parameters, including charges, bonds, angles, and dihedrals. These tools are accessed through the provided GUI, which greatly simplifies the setup and analysis of the underlying calculations. Currently, the toolkit assumes that all QM target data is generated using Gaussian; however, we plan to expand functionality to include alternatives.
To get the most out of the ffTK, a reasonable understanding of the CHARMM and CGenFF force fields is required. For additional information on these topics and the underlying principles of parameterization, users are urged to also visit Alex MacKerell's website for CHARMM FF Parameters and the CHARMM user forums, specifically the parameterization section.
The ffTK plugin relies on a number of other VMD plugins, described in more detail here: Multiplot NAMD Energy Optimization QM Tool Topo Tools
BuildPar is a collection of three tools for identifying missing parameters, building an initial parameter file, and updating the new parameter file based on ffTK output.
Reference parameter sets are loaded from the Load Topology + Parameter Set button, which launches a dialog requesting the location and filename of a topology and parameter file pair. Any non-bonded parameters found within the file pair are loaded into the browser box, providing the element, atom type, parameter values, and the file name from which they came. Multiple parameter sets can be loaded sequentially. Parameters can be restricted to certain elements or parent files using the drop down menus.
To assign the parameters in the input parameter file, select both the target entry from the top pane, and desired reference entry from the bottom pane. The Set from Reference button will copy the reference parameter values to the target entry.IDLEand the optimized charge data is loaded into the Results section. A new PSF file containing the optimized charges can be written by specifying a location and filename in the
Update PSF with new chargesbox, and clicking the Write button. Note that writing a new PSF requires that the PSF and PDB entries are set in the Input section. The results from previous charge optimizations can be reloaded by specifying the ffTK output log file into
Load output file from a previous optimizationand selecting the Load button.
resnameabbreviation for the molecule.
guessedusing an algorithm that assigns charge groups based on chemical equivalency if the PSF/PDB has been loaded into VMD as the TOP molecule (see Input section). The Input section also has a tool to show a variety of labels for each atom to aid in assigning charge groups. The Calculate from TOP button calculates the charge sum using charges found in the PSF, and assumes a neutral molecule. Either of these assumptions can be incorrect, and the user is encouraged to carefully check this number.
Usageabove.
IDLEand optimization data is loaded into the Visualize Results section. Here, the data can be plotted against the QM target data (QME) and the initial MM data that excludes energy contributions from the dihedrals being fit (MMEi). The initial optimization usually requires refinement through the use of the Refine section. Initial optimization is copied to the Refine section by selecting the entry in the Visualize Results box and clicking the Set As Refit Input button. Within the Refine box, various attributes of the optimization can be changed, including dihedral parameter descriptions and optimization settings. The Run Refitting/Refinement button launches the refinement protocol, which is often substantially faster than the original optimization routine. This is because the initial optimization protocol requires a restrained minimization performed on each target datapoint prior to optimization. The relevant dihedral information is stored in
dihAll(see
Reference Datain Visualize Results section), greatly speeding subsequent optimizations/refinements. The user can iteratively adjust dihedral and optimization settings until arriving at an appropriate root-mean-square error (RMSE).