The R.E.D. tools: advances in RESP and ESP charge derivation and force field library building
Top Cited Papers
- 1 January 2010
- journal article
- Published by Royal Society of Chemistry (RSC) in Physical Chemistry Chemical Physics
- Vol. 12 (28), 7821-7839
- https://doi.org/10.1039/c0cp00111b
Abstract
Deriving atomic charges and building a force field library for a new molecule are key steps when developing a force field required for conducting structural and energy-based analysis using molecular mechanics. Derivation of popular RESP charges for a set of residues is a complex and error prone procedure because it depends on numerous input parameters. To overcome these problems, the R.E.D. Tools (RESP and ESP charge Derive, http://q4md-forcefieldtools.org/RED/) have been developed to perform charge derivation in an automatic and straightforward way. The R.E.D. program handles chemical elements up to bromine in the periodic table. It interfaces different quantum mechanical programs employed for geometry optimization and computing molecular electrostatic potential(s), and performs charge fitting using the RESP program. By defining tight optimization criteria and by controlling the molecular orientation of each optimized geometry, charge values are reproduced at any computer platform with an accuracy of 0.0001 e. The charges can be fitted using multiple conformations, making them suitable for molecular dynamics simulations. R.E.D. allows also for defining charge constraints during multiple molecule charge fitting, which are used to derive charges for molecular fragments. Finally, R.E.D. incorporates charges into a force field library, readily usable in molecular dynamics computer packages. For complex cases, such as a set of homologous molecules belonging to a common family, an entire force field topology database is generated. Currently, the atomic charges and force field libraries have been developed for more than fifty model systems and stored in the RESP ESP charge DDataBase. Selected results related to non-polarizable charge models are presented and discussed.Keywords
This publication has 90 references indexed in Scilit:
- CHARMM force field parameters for simulation of reactive intermediates in native and thio‐substituted ribozymesJournal of Computational Chemistry, 2006
- Comparison of multiple Amber force fields and development of improved protein backbone parametersProteins, 2006
- AMBER force-field parameters for phosphorylated amino acids in different protonation states: phosphoserine, phosphothreonine, phosphotyrosine, and phosphohistidineJournal of Molecular Modeling, 2005
- Development and testing of a general amber force fieldJournal of Computational Chemistry, 2004
- A point‐charge force field for molecular mechanics simulations of proteins based on condensed‐phase quantum mechanical calculationsJournal of Computational Chemistry, 2003
- Fast, efficient generation of high‐quality atomic charges. AM1‐BCC model: II. Parameterization and validationJournal of Computational Chemistry, 2002
- Solvated ensemble averaging in the calculation of partial atomic chargesJournal of Computational Chemistry, 2001
- VMD: Visual molecular dynamicsJournal of Molecular Graphics, 1996
- A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP modelThe Journal of Physical Chemistry, 1993
- CHARMM: A program for macromolecular energy, minimization, and dynamics calculationsJournal of Computational Chemistry, 1983