Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Kromann, Jimmy C., Christensen, Anders S., Steinmann, Casper, Korth, Martin, Jensen, Jan H.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2014
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
_version_ 1782324085908307968
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
work_keys_str_mv AT kromannjimmyc athirdgenerationdispersionandthirdgenerationhydrogenbondingcorrectedpm6methodpm6d3h
AT christensenanderss athirdgenerationdispersionandthirdgenerationhydrogenbondingcorrectedpm6methodpm6d3h
AT steinmanncasper athirdgenerationdispersionandthirdgenerationhydrogenbondingcorrectedpm6methodpm6d3h
AT korthmartin athirdgenerationdispersionandthirdgenerationhydrogenbondingcorrectedpm6methodpm6d3h
AT jensenjanh athirdgenerationdispersionandthirdgenerationhydrogenbondingcorrectedpm6methodpm6d3h
AT kromannjimmyc thirdgenerationdispersionandthirdgenerationhydrogenbondingcorrectedpm6methodpm6d3h
AT christensenanderss thirdgenerationdispersionandthirdgenerationhydrogenbondingcorrectedpm6methodpm6d3h
AT steinmanncasper thirdgenerationdispersionandthirdgenerationhydrogenbondingcorrectedpm6methodpm6d3h
AT korthmartin thirdgenerationdispersionandthirdgenerationhydrogenbondingcorrectedpm6methodpm6d3h
AT jensenjanh thirdgenerationdispersionandthirdgenerationhydrogenbondingcorrectedpm6methodpm6d3h