MAB, a generally applicable molecular force field for structure modelling in medicinal chemistry.
The mathematical formulation, parametrization scheme, and structural results of a new, generally applicable molecular force field are presented. The central features are a scheme for automatic parameter assignments, the consistent united-atom approximation, the absence of atom types other than elements, the replacement of electrostatic terms by geometrical hydrogen-bonding terms, the concomitant lack of a need for partial atomic charge assignment and the strict adherence to a finite-range design. As a consequence of omitting all hydrogen atoms, optimal hydrogen-bond patterns are computed dynamically by appropriate network analyses. For a test set of 1589 structures, selected from the Cambridge Structural Database solely on the grounds of a given element list and criteria for high structure refinement, the agreements are on average 2 pm for bonds, 2 degrees for valence angles and 10 to 20 pm for the root-mean-square deviation of atom positions, depending somewhat on size and flexibility of the structures. More qualitative testing of large-scale structural properties of the force field on proteins and DNA oligomers revealed satisfactory performance.
Gerber
P R
PR
F. Hoffmann-La Roche AG, Basel, Switzerland.
Müller
K
K
D003201:Computers; D004247:DNA / Q000737:chemistry; D015195:Drug Design; D004563:Electrochemistry; D006860:Hydrogen Bonding; D008433:Mathematics; D008956:Models, Chemical; D015394:Molecular Structure; D011506:Proteins / Q000737:chemistry; D013816:Thermodynamics
D011506:Proteins; D004247:DNA