Peptide free-energy profile is strongly dependent on the force field: Comparison of C96 and AMBER95

Satoshi Ono; Nobuyuki Nakajima; Junichi Higo; Haruki Nakamura

doi:10.1002/(sici)1096-987x(20000715)21:9<748::aid-jcc4>3.0.co;2-2

Abstract

The C96 and AMBER95 force fields were compared with small model peptides Ac-(Ala)n-NMe (Ac = CH3CO, NMe = NHCH3, 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

Keywords

Force field (fiction)TetrapeptideChemistryAb initioMolecular dynamicsComputational chemistryField (mathematics)Conformational isomerismMoleculePeptidePhysicsQuantum mechanicsOrganic chemistry

Related Publications

Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine “dipeptides” (Ace‐Ala‐Nme and Ace‐Gly‐Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution

Hao Hu , Marcus Elstner , Jan Hermans

Abstract We compare the conformational distributions of Ace‐Ala‐Nme and Ace‐Gly‐Nme sampled in long simulations with several molecular mechanics (MM) force fields and with a fas...

2003 Proteins Structure Function and Bioin... 263 citations

Accurate ab Initio Quantum Chemical Determination of the Relative Energetics of Peptide Conformations and Assessment of Empirical Force Fields

Michael D. Beachy , David Chasman , Robert B. Murphy +2 more

Correlated ab initio calculations have been carried out with a parallel version of the PSGVB electronic structure code to obtain relative energetics of a number of conformations...

1997 Journal of the American Chemical Society 338 citations

How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?

Junmei Wang , Piotr Cieplak , Peter A. Kollman

In this study, we present conformational energies for a molecular mechanical model (Parm99) developed for organic and biological molecules using the restrained electrostatic pot...

2000 Journal of Computational Chemistry 3898 citations

A point‐charge force field for molecular mechanics simulations of proteins based on condensed‐phase quantum mechanical calculations

Yong Duan , Chun Wu , Shibasish Chowdhury +10 more

Abstract Molecular mechanics models have been applied extensively to study the dynamics of proteins and nucleic acids. Here we report the development of a third‐generation point...

2003 Journal of Computational Chemistry 4401 citations

Energy landscape of a peptide consisting of α‐helix, 3<sub>10</sub>‐helix, β‐turn, β‐hairpin, and other disordered conformations

Junichi Higo , Nobutoshi Ito , Masataka Kuroda +3 more

Abstract The energy landscape of a peptide [Ace‐Lys‐Gln‐Cys‐Arg‐Glu‐Arg‐Ala‐Nme] in explicit water was studied with a multicanonical molecular dynamics simulation, and the AMBER...

2001 Protein Science 79 citations

Publication Info

Year: 2000
Type: article
Volume: 21
Issue: 9
Pages: 748-762
Citations: 61
Access: Closed

External Links

Download PDF (Free) View on DOI.org Semantic Scholar

Social Impact

Altmetric

Peptide free-energy profile is strongly dependent on the force field: Comparison of C96 and AMBER95

PlumX Metrics

Social media, news, blog, policy document mentions

Citation Metrics

OpenAlex

Influential

CrossRef

Cite This

APA Style

                            
                                
                                    Satoshi Ono, 
                                
                                    Nobuyuki Nakajima, 
                                
                                    Junichi Higo
                                
                                et al.
                            
                            (2000). 
                            Peptide free-energy profile is strongly dependent on the force field: Comparison of C96 and AMBER95. 
                            Journal of Computational Chemistry
                            , 21
                            (9)
                            , 748-762.
                            https://doi.org/10.1002/(sici)1096-987x(20000715)21:9<748::aid-jcc4>3.0.co;2-2
                        

Identifiers

DOI: 10.1002/(sici)1096-987x(20000715)21:9<748::aid-jcc4>3.0.co;2-2

Data Quality

Data completeness: 77%