Abstract
The MFCC-downhill simplex method is presented to study the binding structure of small ligands in large molecular complex systems. This method employs the Molecular Fractionation with Conjugated Caps (MFCC) approach to compute the interaction energy-structure relation of the system and implements the downhill simplex algorithm for structural optimization. The method is tested on a molecular system of cyclo-AAGAGGH2O to optimize the binding position of water molecule to the fixed cyclohexapeptide. The MFCC-downhill simplex optimization results are in good agreement with the crystal structure. An MFCC-Powell optimization method which uses the Powell's minimization algorithm is also described and tested on the same system. The MFCC-downhill simplex optimization is more efficient than the MFCC-Powell method.
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