Premium
Peptide free‐energy profile is strongly dependent on the force field: Comparison of C96 and AMBER95
Author(s) -
Ono Satoshi,
Nakajima Nobuyuki,
Higo Junichi,
Nakamura Haruki
Publication year - 2000
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/(sici)1096-987x(20000715)21:9<748::aid-jcc4>3.0.co;2-2
Subject(s) - force field (fiction) , tetrapeptide , chemistry , ab initio , molecular dynamics , computational chemistry , field (mathematics) , conformational isomerism , molecule , peptide , physics , quantum mechanics , organic chemistry , biochemistry , mathematics , pure mathematics
The C96 and AMBER95 force fields were compared with small model peptides Ac‐(Ala) n ‐NMe (Ac = CH 3 CO, NMe = NHCH 3 , n =2 and 3) in vacuo and in TIP3P water by computing the free‐energy profiles using multicanonical molecular dynamics method. The C96 force field is a modified version of the AMBER95 force field, which was adjusted to reproduce the energy difference between extended β‐ and constrained α‐helical energies for the alanine tetrapeptide, obtained by the high level ab initio MO method. The slight modification resulted in a large difference in the free energy profiles. The C96 force field prefers relatively extended conformers, whereas the AMBER95 force field favors turn conformations. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 748–762, 2000