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Inclusion of solvation free energy with molecular mechanics energy: Alanyl dipeptide as a test case
Author(s) -
Schiffer Celia A.,
Caldwell James W.,
Stroud Robert M.,
Kollman Peter A.
Publication year - 1992
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1002/pro.5560010311
Subject(s) - dipeptide , molecular mechanics , solvation , inclusion (mineral) , computational chemistry , chemistry , energy (signal processing) , chemical physics , molecular dynamics , physics , thermodynamics , molecule , quantum mechanics , biochemistry , organic chemistry , peptide
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 .