ArticlePhysical chemistry chemical physics : PCCP2010
The R.E.D. tools: advances in RESP and ESP charge derivation and force field library building.
Article in Physical chemistry chemical physics : PCCP, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 270 papers.
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270 citing papers in PubMed.
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- Deep Eutectic Solvent Interaction with Graphene Oxide: A Combined Experimental and Molecular Dynamics Characterization.The journal of physical chemistry. B · 2025Article
- Photoinduced chromophore dissociation resulting in aggregation-induced red fluorescence.Communications biology · 2025Article
- Dynamic Behavior and Substrate Interactions of the Polymyxin Resistance Determinant MCR-1 Investigated by Molecular Dynamics Simulations in the Membrane Environment.Journal of chemical information and modeling · 2025Article
- The Influence of pH on the Catalytic Capacity of Levodopa in the Electroreduction Processes of ZnMolecules (Basel, Switzerland) · 2025Article
- Article
- Evaluating the Functional Importance of Conformer-Dependent Atomic Partial Charge Assignment.Journal of computational chemistry · 2025Article
- Shock Wave-Induced Degradation of Polyethylene and Polystyrene: A Reactive Molecular Dynamics Study on Nanoplastic Transformation in Aqueous Environments.Molecules (Basel, Switzerland) · 2025Article
- Passive Transport across Cell Membranes beyond the Overton Rule: Insights from Solute Exchange in Vesicles and Molecular Dynamics of Atropisomers.ACS applied materials & interfaces · 2025Article
210 more citing papers are in PubMed but not listed here.
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9 authors.
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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, ) 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.
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