Skip to main content

Lund University Publications

LUND UNIVERSITY LIBRARIES

Prediction of hydration free energies for the SAMPL4 data set with the AMOEBA polarizable force field.

Manzoni, Francesco LU and Söderhjelm, Pär LU (2014) In Journal of Computer-Aided Molecular Design 28(3). p.235-244
Abstract
Hydration free energy calculations are often used to validate molecular simulation methodologies and molecular mechanics force fields. We use the free-energy perturbation method together with the AMOEBA polarizable force field and the Poltype parametrization protocol to predict the hydration free energies of 52 molecules as part of the SAMPL4 blind challenge. For comparison, similar calculations are performed using the non-polarizable General Amber force field. Against our expectations, the latter force field gives the better results compared to experiment. One possible explanation is the sensitivity of the AMOEBA results to the conformation used for parametrization.
Please use this url to cite or link to this publication:
author
and
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Journal of Computer-Aided Molecular Design
volume
28
issue
3
pages
235 - 244
publisher
Springer
external identifiers
  • pmid:24577872
  • wos:000335233100009
  • scopus:84899988670
  • pmid:24577872
ISSN
1573-4951
DOI
10.1007/s10822-014-9733-3
language
English
LU publication?
yes
additional info
The information about affiliations in this record was updated in December 2015. The record was previously connected to the following departments: Theoretical Chemistry (S) (011001039)
id
99955ef2-7e46-4c77-b417-6c59af552287 (old id 4387377)
date added to LUP
2016-04-01 10:58:30
date last changed
2021-07-13 02:32:59
@article{99955ef2-7e46-4c77-b417-6c59af552287,
  abstract     = {Hydration free energy calculations are often used to validate molecular simulation methodologies and molecular mechanics force fields. We use the free-energy perturbation method together with the AMOEBA polarizable force field and the Poltype parametrization protocol to predict the hydration free energies of 52 molecules as part of the SAMPL4 blind challenge. For comparison, similar calculations are performed using the non-polarizable General Amber force field. Against our expectations, the latter force field gives the better results compared to experiment. One possible explanation is the sensitivity of the AMOEBA results to the conformation used for parametrization.},
  author       = {Manzoni, Francesco and Söderhjelm, Pär},
  issn         = {1573-4951},
  language     = {eng},
  number       = {3},
  pages        = {235--244},
  publisher    = {Springer},
  series       = {Journal of Computer-Aided Molecular Design},
  title        = {Prediction of hydration free energies for the SAMPL4 data set with the AMOEBA polarizable force field.},
  url          = {http://dx.doi.org/10.1007/s10822-014-9733-3},
  doi          = {10.1007/s10822-014-9733-3},
  volume       = {28},
  year         = {2014},
}