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Protein Science, Vol 1, Issue 3 396-400, Copyright © 1992 by Cold Spring Harbor Laboratory Press

ARTICLE

Inclusion of solvation free energy with molecular mechanics energy: Alanyl dipeptide as a test case

C. A. SCHIFFER, J. W. CALDWELL, R. M. STROUD and P. A. KOLLMAN
Department of Biochemistry and Biophysics, Graduate Group in Biophysics San Francisco, California 94143

A combined force field of molecular mechanics and solvation free energy is tested by carrying out energy minimization and molecular dynamics on several conformations of the alanyl dipeptide. Our results are qualitatively consistent with previous experimental and computational studies, in that the addition of solvation energy stabilizes the C(5) conformation of the alanyl dipeptide relative to the C(7).
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