The effective fragment molecular orbital method for fragments connected by covalent bonds.
We extend the effective fragment molecular orbital method (EFMO) into treating fragments connected by covalent bonds. The accuracy of EFMO is compared to FMO and conventional ab initio electronic structure methods for polypeptides including proteins. Errors in energy for RHF and MP2 are within 2 kca...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2012-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC3402534?pdf=render |
| _version_ | 1818574369015726080 |
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| author | Casper Steinmann Dmitri G Fedorov Jan H Jensen |
| author_facet | Casper Steinmann Dmitri G Fedorov Jan H Jensen |
| author_sort | Casper Steinmann |
| collection | DOAJ |
| description | We extend the effective fragment molecular orbital method (EFMO) into treating fragments connected by covalent bonds. The accuracy of EFMO is compared to FMO and conventional ab initio electronic structure methods for polypeptides including proteins. Errors in energy for RHF and MP2 are within 2 kcal/mol for neutral polypeptides and 6 kcal/mol for charged polypeptides similar to FMO but obtained two to five times faster. For proteins, the errors are also within a few kcal/mol of the FMO results. We developed both the RHF and MP2 gradient for EFMO. Compared to ab initio, the EFMO optimized structures had an RMSD of 0.40 and 0.44 Å for RHF and MP2, respectively. |
| first_indexed | 2024-12-15T00:25:41Z |
| format | Article |
| id | doaj.art-6b15af8c1652470f9578d0aeab049eda |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-15T00:25:41Z |
| publishDate | 2012-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-6b15af8c1652470f9578d0aeab049eda2022-12-21T22:42:10ZengPublic Library of Science (PLoS)PLoS ONE1932-62032012-01-0177e4111710.1371/journal.pone.0041117The effective fragment molecular orbital method for fragments connected by covalent bonds.Casper SteinmannDmitri G FedorovJan H JensenWe extend the effective fragment molecular orbital method (EFMO) into treating fragments connected by covalent bonds. The accuracy of EFMO is compared to FMO and conventional ab initio electronic structure methods for polypeptides including proteins. Errors in energy for RHF and MP2 are within 2 kcal/mol for neutral polypeptides and 6 kcal/mol for charged polypeptides similar to FMO but obtained two to five times faster. For proteins, the errors are also within a few kcal/mol of the FMO results. We developed both the RHF and MP2 gradient for EFMO. Compared to ab initio, the EFMO optimized structures had an RMSD of 0.40 and 0.44 Å for RHF and MP2, respectively.http://europepmc.org/articles/PMC3402534?pdf=render |
| spellingShingle | Casper Steinmann Dmitri G Fedorov Jan H Jensen The effective fragment molecular orbital method for fragments connected by covalent bonds. PLoS ONE |
| title | The effective fragment molecular orbital method for fragments connected by covalent bonds. |
| title_full | The effective fragment molecular orbital method for fragments connected by covalent bonds. |
| title_fullStr | The effective fragment molecular orbital method for fragments connected by covalent bonds. |
| title_full_unstemmed | The effective fragment molecular orbital method for fragments connected by covalent bonds. |
| title_short | The effective fragment molecular orbital method for fragments connected by covalent bonds. |
| title_sort | effective fragment molecular orbital method for fragments connected by covalent bonds |
| url | http://europepmc.org/articles/PMC3402534?pdf=render |
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