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Parametrizing a polarizable force field from ab initio data. I. The fluctuating point charge model
Abstract
We have developed a polarizable force field for peptides, using all-atom OPLS (OPLS-AA) nonelectrostatic terms and electrostatics based on a fluctuating charge model and fit to ab initio calculations of polarization responses. We discuss the fitting procedure, and specific techniques we have developed that are necessary in order to obtain an accurate, stable model. Our model is comparable to the best existing molecular mechanics force fields in reproducing quantum-chemical peptide energetics. It also accurately reproduces many-body effects in many cases. We believe that straightforward extensions of our linear-response electrostatic model will significantly improve the accuracy for those cases that the present model does not adequately address.
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Citations
Cited by
Combining Machine Learning and Computational Chemistry for Predictive Insights Into Chemical Systems
Keith, J. A., Vassilev-Galindo, V., Cheng, B., Chmiela, S., Gastegger, M., Müller, K.-R., & Tkatchenko, A. (2021) · Chemical Reviews · doi:10.1021/acs.chemrev.1c00107 · Cited by 849
Molecular Recognition and Docking Algorithms
Brooijmans, N., & Kuntz, I. D. (2003) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.biophys.32.110601.142532 · Cited by 788
Biomolecular Modeling: Goals, Problems, Perspectives
van Gunsteren, W. F., Bakowies, D., Baron, R., Chandrasekhar, I., Christen, M., Daura, X., Gee, P., Geerke, D. P., Glättli, A., Hünenberger, P. H., et al. (2006) · Angewandte Chemie International Edition · doi:10.1002/anie.200502655 · Cited by 561
Christensen, A. S., Kubař, T., Cui, Q., & Elstner, M. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.5b00584 · Cited by 446
Polarizable Force Field for Peptides and Proteins Based on the Classical Drude Oscillator
Lopes, P. E. M., Huang, J., Shim, J., Luo, Y., Li, H., Roux, B., & MacKerell, A. D. (2013) · Journal of Chemical Theory and Computation · doi:10.1021/ct400781b · Cited by 386
Metadata
- Authors
- Banks, J. L., Kaminski, G. A., Zhou, R., Mainz, D. T., Berne, B. J., & Friesner, R. A.
- Venue
- The Journal of Chemical Physics
- Publisher
- AIP Publishing
- Published
- 1999-01-08
- Volume
- 110
- Issue
- 2
- Pages
- 741-754
- ISSN
- 0021-9606 (ISSN-L)
- 1089-7690
- OpenAlex
- W2031920211
- Cited by
- 253
- References
- 0
- FWCI
- 4.46
- Type
- journal article
- Language
- en
- Open access
- closed
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- Banks, J. L., Kaminski, G. A., Zhou, R., Mainz, D. T., Berne, B. J., & Friesner, R. A. (1999). Parametrizing a polarizable force field from ab initio data. I. The fluctuating point charge model. The Journal of Chemical Physics. https://doi.org/10.1063/1.478043
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
