𝔖 Bobbio Scriptorium
✦   LIBER   ✦

Combination of the CHARMM27 force field with united-atom lipid force fields

✍ Scribed by Nicolas Sapay; D. Peter Tieleman

Publisher
John Wiley and Sons
Year
2010
Tongue
English
Weight
514 KB
Volume
32
Category
Article
ISSN
0192-8651

No coin nor oath required. For personal study only.

✦ Synopsis

Abstract

Computer simulations offer a valuable way to study membrane systems, from simple lipid bilayers to large transmembrane protein complexes and lipid‐nucleic acid complexes for drug delivery. Their accuracy depends on the quality of the force field parameters used to describe the components of a particular system. We have implemented the widely used CHARMM22 and CHARMM27 force fields in the GROMACS simulation package to (i) combine the CHARMM22 protein force field with two sets of united‐atom lipids parameters; (ii) allow comparisons of the lipid CHARMM27 force field with other lipid force fields or lipid‐protein force field combinations. Our tests do not show any particular issue with the combination of the all‐atom CHARMM22 force field with united‐atoms lipid parameters, although pertinent experimental data are lacking to assess the quality of the lipid‐protein interactions. The conversion utilities allow automatic generation of GROMACS simulation files with CHARMM nucleic acids and protein parameters and topologies, starting from pdb files using the standard GROMACS pdb2gmx method. CMAP is currently not implemented. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010

📜 SIMILAR VOLUMES

CHARMM general force field: A force fiel
CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields
✍ K. Vanommeslaeghe; E. Hatcher; C. Acharya; S. Kundu; S. Zhong; J. Shim; E. Daria 📂 Article 📅 2009 🏛 John Wiley and Sons 🌐 English ⚖ 643 KB

## Abstract The widely used CHARMM additive all‐atom force field includes parameters for proteins, nucleic acids, lipids, and carbohydrates. In the present article, an extension of the CHARMM force field to drug‐like molecules is presented. The resulting CHARMM General Force Field (CGenFF) covers a

Modification of the CHARMM force field f
Modification of the CHARMM force field for DMPC lipid bilayer
✍ Carl-Johan Högberg; Alexei M. Nikitin; Alexander P. Lyubartsev 📂 Article 📅 2008 🏛 John Wiley and Sons 🌐 English ⚖ 897 KB

## Abstract The CHARMM force field for DMPC lipids was modified in order to improve agreement with experiment for a number of important properties of hydrated lipid bilayer. The modification consists in introduction of a scaling factor 0.83 for 1–4 electrostatic interactions (between atoms separate

Symmetrization of the AMBER and CHARMM f
Symmetrization of the AMBER and CHARMM force fields
✍ Edyta Małolepsza; Birgit Strodel; Mey Khalili; Semen Trygubenko; Szilard N. Feje 📂 Article 📅 2010 🏛 John Wiley and Sons 🌐 English ⚖ 380 KB

## Abstract The AMBER and CHARMM force fields are analyzed from the viewpoint of the permutational symmetry of the potential for feasible exchanges of identical atoms and chemical groups in amino and nucleic acids. In each case, we propose schemes for symmetrizing the potentials, which greatly faci

Fast docking using the CHARMM force fiel
Fast docking using the CHARMM force field with EADock DSS
✍ Aurélien Grosdidier; Vincent Zoete; Olivier Michielin 📂 Article 📅 2011 🏛 John Wiley and Sons 🌐 English ⚖ 565 KB

## Abstract The prediction of binding modes (BMs) occurring between a small molecule and a target protein of biological interest has become of great importance for drug development. The overwhelming diversity of needs leaves room for docking approaches addressing specific problems. Nowadays, the un

Validation of the general purpose QUANTA
Validation of the general purpose QUANTA ®3.2/CHARMm® force field
✍ Frank A. Momany; Rebecca Rone 📂 Article 📅 1992 🏛 John Wiley and Sons 🌐 English ⚖ 949 KB

An evaluation of the CHARMm force field for small molecules is described. Using different force field conditions and computational techniques, a wide variety of compounds are analyzed. rms deviations of Cartesian coordinates for 49 diverse organic molecules taken from the Cambridge Crystallographic

Parametrization of aliphatic CHn united
Parametrization of aliphatic CHn united atoms of GROMOS96 force field
✍ Daura, Xavier; Mark, Alan E.; Van Gunsteren, Wilfred F. 📂 Article 📅 1998 🏛 John Wiley and Sons 🌐 English ⚖ 203 KB

The derivation of the van der Waals parameters for the aliphatic CH united atoms of the GROMOS96 force field is presented. The parameters n have been adjusted to reproduce the experimental enthalpies of vaporization and vapor pressures or densities of a set of nine alkanes in the liquid state at 298