We present the derivation of a new molecular mechanical force field for simulating the
structures, conformational energies, and interaction energies of proteins, nucleic acids, and …

We describe here a general Amber force field (GAFF) for organic molecules. GAFF is
designed to be compatible with existing Amber force fields for proteins and nucleic acids …

In molecular mechanics (MM) studies, atom types and/or bond types of molecules are
needed to determine prior to energy calculations. We present here an automatic algorithm of …

Knowledge of the charge distribution within molecules is es-sential for determining the
electrostatic energies (including hy-drogen bonding) in molecular mechanics and molecular …

We present an all atom potential energy function for the simulation of proteins and nucleic
acids. This work is an extension of the CH united atom function recently presented by SJ …

The high affinity of the noncovalent interaction between biotin and streptavidin forms the
basis for many diagnostic assays that require the formation of an irreversible and specific …

We report a reparameterization of the glycosidic torsion χ of the Cornell et al. AMBER force
field for RNA, χOL. The parameters remove destabilization of the anti region found in the ff99 …

The spontaneous spreading (called superspreading) of aqueous trisiloxane ethoxylate
surfactant solutions on hydrophobic solid surfaces is a fascinating phenomenon with several …

This paper explores the premise that insights gained from studying the well-characterized
van der Waals (vdW) interactions of rare-gas atoms can be used advantageously …

Nucleic acidparameters are developed for the all-atomempirical energy function used in the
CHARMM program. The parameters were determined by use of results for model …