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A third-generation dispersion and third-generation hydrogen bonding corrected PM6 method: PM6-D3H+
We present new dispersion and hydrogen bond corrections to the PM6 method, PM6-D3H+, and its implementation in the GAMESS program. The method combines the DFT-D3 dispersion correction by Grimme et al. with a modified version of the H+ hydrogen bond correction by Korth. Overall, the interaction energ...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
PeerJ Inc.
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4081274/ https://www.ncbi.nlm.nih.gov/pubmed/25024918 http://dx.doi.org/10.7717/peerj.449 |
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author | Kromann, Jimmy C. Christensen, Anders S. Steinmann, Casper Korth, Martin Jensen, Jan H. |
author_facet | Kromann, Jimmy C. Christensen, Anders S. Steinmann, Casper Korth, Martin Jensen, Jan H. |
author_sort | Kromann, Jimmy C. |
collection | PubMed |
description | We present new dispersion and hydrogen bond corrections to the PM6 method, PM6-D3H+, and its implementation in the GAMESS program. The method combines the DFT-D3 dispersion correction by Grimme et al. with a modified version of the H+ hydrogen bond correction by Korth. Overall, the interaction energy of PM6-D3H+ is very similar to PM6-DH2 and PM6-DH+, with RMSD and MAD values within 0.02 kcal/mol of one another. The main difference is that the geometry optimizations of 88 complexes result in 82, 6, 0, and 0 geometries with 0, 1, 2, and 3 or more imaginary frequencies using PM6-D3H+ implemented in GAMESS, while the corresponding numbers for PM6-DH+ implemented in MOPAC are 54, 17, 15, and 2. The PM6-D3H+ method as implemented in GAMESS offers an attractive alternative to PM6-DH+ in MOPAC in cases where the LBFGS optimizer must be used and a vibrational analysis is needed, e.g., when computing vibrational free energies. While the GAMESS implementation is up to 10 times slower for geometry optimizations of proteins in bulk solvent, compared to MOPAC, it is sufficiently fast to make geometry optimizations of small proteins practically feasible. |
format | Online Article Text |
id | pubmed-4081274 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | PeerJ Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-40812742014-07-14 A third-generation dispersion and third-generation hydrogen bonding corrected PM6 method: PM6-D3H+ Kromann, Jimmy C. Christensen, Anders S. Steinmann, Casper Korth, Martin Jensen, Jan H. PeerJ Biochemistry We present new dispersion and hydrogen bond corrections to the PM6 method, PM6-D3H+, and its implementation in the GAMESS program. The method combines the DFT-D3 dispersion correction by Grimme et al. with a modified version of the H+ hydrogen bond correction by Korth. Overall, the interaction energy of PM6-D3H+ is very similar to PM6-DH2 and PM6-DH+, with RMSD and MAD values within 0.02 kcal/mol of one another. The main difference is that the geometry optimizations of 88 complexes result in 82, 6, 0, and 0 geometries with 0, 1, 2, and 3 or more imaginary frequencies using PM6-D3H+ implemented in GAMESS, while the corresponding numbers for PM6-DH+ implemented in MOPAC are 54, 17, 15, and 2. The PM6-D3H+ method as implemented in GAMESS offers an attractive alternative to PM6-DH+ in MOPAC in cases where the LBFGS optimizer must be used and a vibrational analysis is needed, e.g., when computing vibrational free energies. While the GAMESS implementation is up to 10 times slower for geometry optimizations of proteins in bulk solvent, compared to MOPAC, it is sufficiently fast to make geometry optimizations of small proteins practically feasible. PeerJ Inc. 2014-06-19 /pmc/articles/PMC4081274/ /pubmed/25024918 http://dx.doi.org/10.7717/peerj.449 Text en © 2014 Kromann et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited. |
spellingShingle | Biochemistry Kromann, Jimmy C. Christensen, Anders S. Steinmann, Casper Korth, Martin Jensen, Jan H. A third-generation dispersion and third-generation hydrogen bonding corrected PM6 method: PM6-D3H+ |
title | A third-generation dispersion and third-generation hydrogen bonding corrected PM6 method: PM6-D3H+ |
title_full | A third-generation dispersion and third-generation hydrogen bonding corrected PM6 method: PM6-D3H+ |
title_fullStr | A third-generation dispersion and third-generation hydrogen bonding corrected PM6 method: PM6-D3H+ |
title_full_unstemmed | A third-generation dispersion and third-generation hydrogen bonding corrected PM6 method: PM6-D3H+ |
title_short | A third-generation dispersion and third-generation hydrogen bonding corrected PM6 method: PM6-D3H+ |
title_sort | third-generation dispersion and third-generation hydrogen bonding corrected pm6 method: pm6-d3h+ |
topic | Biochemistry |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4081274/ https://www.ncbi.nlm.nih.gov/pubmed/25024918 http://dx.doi.org/10.7717/peerj.449 |
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