Force Field Improvement for Conformational Analysis of Arylamine-Substituted Dinucleotides

摘要

Several changes were made in Alligner's MMPI molecular mechanics program in preparation for calculating the conformation of DNA adducts in Experiment 6289. The following improvements were accomplished: The MMS dihedral driver was added to MMPI, to allow two angles to be manipulated simultaneously. In addition, the new driver provides two fundamentally different methods for performing the desired dihedral rotations. A 'pseudorotation driver' was added, which allows a furanose ring to be moved along a pseudorotation pathway of puckering. Various errors in the original program were corrected and the user's options for regulating the amount of output were increased. A series of calculations on conjugated hydrocarbons was performed to compare the calculations of the hybrid program with other calculations and with experimental measurement.