Harmonic Force Constants for Molecular Mechanics Force Fields via Hessian Matrix Projection
A modification to the Seminario method [ Int. J. Quantum Chem. 1996, 60, 1271−1277 ] is proposed, which derives accurate harmonic bond and angle molecular mechanics force field parameters directly from the quantum mechanical Hessian matrix. The new method reduces the average error in the reproductio...
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| Published in: | Journal of chemical theory and computation Vol. 14; no. 1; pp. 274 - 281 |
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| Format: | Journal Article |
| Language: | English |
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09-01-2018
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| Abstract | A modification to the Seminario method [ Int. J. Quantum Chem. 1996, 60, 1271−1277 ] is proposed, which derives accurate harmonic bond and angle molecular mechanics force field parameters directly from the quantum mechanical Hessian matrix. The new method reduces the average error in the reproduction of quantum mechanical normal-mode frequencies of a benchmark set of 70 molecules from 12.3% using the original method, to 6.3%. The modified Seminario method is fully automated, and all parameters are computed directly from quantum mechanical data, thereby avoiding interdependency between bond and angle parameters and other components of the force field. A complete set of bond and angle force field parameters for the 20 naturally occurring amino acids is also provided for use in the future development of protein force fields. |
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| AbstractList | A modification to the Seminario method [ Int. J. Quantum Chem. 1996 , 60 , 1271 - 1277 ] is proposed, which derives accurate harmonic bond and angle molecular mechanics force field parameters directly from the quantum mechanical Hessian matrix. The new method reduces the average error in the reproduction of quantum mechanical normal-mode frequencies of a benchmark set of 70 molecules from 12.3% using the original method, to 6.3%. The modified Seminario method is fully automated, and all parameters are computed directly from quantum mechanical data, thereby avoiding interdependency between bond and angle parameters and other components of the force field. A complete set of bond and angle force field parameters for the 20 naturally occurring amino acids is also provided for use in the future development of protein force fields. A modification to the Seminario method [ Int. J. Quantum Chem. 1996, 60, 1271−1277 ] is proposed, which derives accurate harmonic bond and angle molecular mechanics force field parameters directly from the quantum mechanical Hessian matrix. The new method reduces the average error in the reproduction of quantum mechanical normal-mode frequencies of a benchmark set of 70 molecules from 12.3% using the original method, to 6.3%. The modified Seminario method is fully automated, and all parameters are computed directly from quantum mechanical data, thereby avoiding interdependency between bond and angle parameters and other components of the force field. A complete set of bond and angle force field parameters for the 20 naturally occurring amino acids is also provided for use in the future development of protein force fields. |
| Author | Allen, Alice E. A Payne, Michael C Cole, Daniel J |
| AuthorAffiliation | TCM Group, Cavendish Laboratory School of Natural and Environmental Sciences |
| AuthorAffiliation_xml | – name: School of Natural and Environmental Sciences – name: TCM Group, Cavendish Laboratory |
| Author_xml | – sequence: 1 givenname: Alice E. A orcidid: 0000-0002-8727-8333 surname: Allen fullname: Allen, Alice E. A organization: TCM Group, Cavendish Laboratory – sequence: 2 givenname: Michael C surname: Payne fullname: Payne, Michael C organization: TCM Group, Cavendish Laboratory – sequence: 3 givenname: Daniel J orcidid: 0000-0003-2933-0719 surname: Cole fullname: Cole, Daniel J email: daniel.cole@ncl.ac.uk organization: School of Natural and Environmental Sciences |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/29161029$$D View this record in MEDLINE/PubMed |
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| SubjectTerms | Amino acids Chemical bonds Hessian matrices Molecular chains Parameter modification Proteins Quantum mechanics |
| Title | Harmonic Force Constants for Molecular Mechanics Force Fields via Hessian Matrix Projection |
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