MATCH: An atom‐typing toolset for molecular mechanics force fields

Abstract

We introduce a toolset of program libraries collectively titled MATCH (Multipurpose Atom-Typer for CHARMM) for the automated assignment of atom types and force field parameters for molecular mechanics simulation of organic molecules. The toolset includes utilities for the conversion from multiple chemical structure file formats into a molecular graph. A general chemical pattern-matching engine using this graph has been implemented whereby assignment of molecular mechanics atom types, charges and force field parameters is achieved by comparison against a customizable list of chemical fragments. While initially designed to complement the CHARMM simulation package and force fields by generating the necessary input topology and atom-type data files, MATCH can be expanded to any force field and program, and has core functionality that makes it extendable to other applications such as fragment-based property prediction. In the present work, we demonstrate the accurate construction of atomic parameters of molecules within each force field included in CHARMM36 through exhaustive cross validation studies illustrating that bond increment rules derived from one force field can be transferred to another. In addition, using leave-one-out substitution it is shown that it is also possible to substitute missing intra and intermolecular parameters with ones included in a force field to complete the parameterization of novel molecules. Finally, to demonstrate the robustness of MATCH and the coverage of chemical space offered by the recent CHARMM CGENFF force field (Vanommeslaeghe, et al., JCC., 2010, 31, 671–690), one million molecules from the PubChem database of small molecules are typed, parameterized and minimized.

Ligand Modulation of Sidechain Dynamics in a Wild-Type Human GPCR

“…CHARMMsuitable parameters for NECA and ZM241385 compounds were generated with the program MATCH (Yesselman et al, 2012). Molecular constructs were initially equilibrated using a two-phase protocol implemented by us earlier for MD simulations of leucine transporter (LeuT)/micelle complexes (Khelashvili et al, 2013;LeVine et al, 2016): (i) short energy minimization was carried out during which protein, water, and ion atoms were fixed and the coordinates of only DDM molecules were allowed to evolve freely; and (ii) 1.5 ns long MD simulations were conducted with the protein backbone harmonically constrained.…”

Automatic GROMACS Topology Generation and Comparisons of Force Fields for Solvation Free Energy Calculations

“…We have limited this analysis to the SPC/E water model and summarize some of the molecules with relatively high mean unsigned error in Tables 8 through 16. Note that the CGenFF parameters were assigned using MATCH 30 and that there might be differences to parameters assigned using the CGenFF program 32,33 . Table 8: Parameters of 1-chlorohexane in three different force fields, and the B3LYP/PCM charge model used with GAFF, taking polarization costs into account.…”

Quantum‐Assisted Metrology of Neutral Vitamins in the Gas Phase

“…The conformational space was scanned by an MD simulation using the LAMMPS package22 with CHARMM23 force field parameters obtained from the multipurpose atom typer for CHARMM 24. During the MD simulation, a single molecule was propagated over 100 ns (after an equilibration run of 10 ns) in time steps of 1 fs at the respective experimental oven temperatures of around 450 K controlled by a Nosé–Hoover thermostat25 with a relaxation time of 0.1 ps.…”