Background

A central issue with classical simulations concerns the accuracy and predictive value of the force field used to generate them. Providing a range of tools and services associated with the construction, parameterization, and optimization of empirical atomic force fields used in biomolecular computations is a primary aim of the CMC. Four types of potential functions are commonly utilized in most biomolecular computations: Coarse-grained (CG), extended atom, all-atom non-polarizable, and all-atom polarizable.

All-atom force fields are mathematical objects constructed from simple analytical functions parameterized to approximate the Born-Oppenheimer potential energy surface and reproduce known experimental observables. Parameters for the all-atom additive nonpolarizable CHARMM potential functions are currently available for amino acids, nucleic acids and common phospholipids.

All this is insufficient to accurately reproduce/explain a wealth of experimental data on membrane proteins. Accurate potential functions will also be required for a growing number of novel spectroscopic probes, e.g., nitroxide spin labels, modified residues, uncommon lipids, as well as various ligands and inhibitors. This list is expected to grow as a result of the research conducted within the Bridging Projects.

Goals

1. Automatically generate, test and validate the all-atom nonpolarizable / drude polarizable force fields used in MD simulations.

2. Make archives for all molecules parameterized by this server and set up a database for users' search and download