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Aromatic Stacking

John Parkinson ECPT johnny at wadham.chem.ed.ac.uk
Thu May 22 06:37:45 EST 1997

I'm attempting to simulate dynamics involving the insertion of a benzene
ring into an aromatic pocket within a protein. Has anyone come up with any
reasonable 'fixes' to account for aromatic stacking interactions which
will hold the ring within the pocket ? I have attempted increasing the
dispersive forces associated with the carbons on the appropriate aromatics
without much success. Short of altering the xplor source code, has
anyone got any ideas of how to introduce such an energy term ?


John Parkinson

Edinburgh Centre for Protein Technology
Joseph Black Chemistry Building, The King's Buildings
West Mains Road, Edinburgh EH9 3JJ, UK

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