Inclusion of solvation free energy with molecular mechanics energy: alanyl dipeptide as a test case.
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 C5 conformation of the alanyl dipeptide relative to the C7.
Schiffer
C A
CA
Department of Biochemistry and Biophysics, University of California, San Francisco 94143.
Caldwell
J W
JW
Stroud
R M
RM
Kollman
P A
PA
D002151:Calorimetry; D004151:Dipeptides / Q000737:chemistry*; D008956:Models, Chemical; D011487:Protein Conformation; D011789:Quantum Theory; D013816:Thermodynamics
D004151:Dipeptides; C002956:alanylalanine