I'm going on the assumption that there are no 'silly questions'...
How would one calculate the energy difference between a north conformation and a south conformation of a nucleoside in solution? Clearly, one could build a periodic box of H2O for each structure and optimize, but wouldn't the water energy dominate? One could delete the water molecules, but now that's a vacuum calculation. Let's assume using a distance-dependent dielectric is not going to give realistic values. Perhaps a solvent model, like GB or PB?
Steve
Steven M. Graham. Ph.D.
Associate Professor
Department of Chemistry
St. John's University
8000 Utopia Parkway
Queens, NY 11439
718-990-5217
grahams.stjohns.edu
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Received on Sun Jun 24 2012 - 11:00:03 PDT
