Source:http://linkedlifedata.com/resource/pubmed/id/17330884
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| Predicate | Object |
|---|---|
| rdf:type | |
| lifeskim:mentions | |
| pubmed:issue |
9
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| pubmed:dateCreated |
2007-5-2
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| pubmed:abstractText |
The three-body energy expansion in the fragment molecular orbital method (FMO) was applied to the 2nd order Møller-Plesset theory (MP2). The accuracy of both the two and three-body expansions was determined for water clusters, alanine n-mers (alpha-helices and beta-strands) and one synthetic protein, using the 6-31G* and 6-311G* basis sets. At the best level of theory (three-body, two molecules/residues per fragment), the absolute errors in energy relative to ab initio MP2 were at most 1.2 and 5.0 mhartree, for the 6-31G* and 6-311G* basis sets, respectively. The relative accuracy was at worst 99.996% and 99.96%, for 6-31G* and 6-311G*, respectively. A three-body approximation was introduced and the optimum threshold value was determined. The protein calculation (6-31G*) at the production level (FMO2/2) took 3 h on 36 3.2-GHz Pentium 4 nodes and had the absolute error in the MP2 correlation energy of only 2 kcal/mol.
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| pubmed:language |
eng
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| pubmed:journal | |
| pubmed:status |
PubMed-not-MEDLINE
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| pubmed:month |
Jul
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| pubmed:issn |
0192-8651
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| pubmed:author | |
| pubmed:copyrightInfo |
Copyright (c) 2007 Wiley Periodicals, Inc.
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| pubmed:issnType |
Print
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| pubmed:day |
15
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| pubmed:volume |
28
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| pubmed:owner |
NLM
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| pubmed:authorsComplete |
Y
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| pubmed:pagination |
1476-84
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| pubmed:year |
2007
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| pubmed:articleTitle |
Accuracy of the three-body fragment molecular orbital method applied to Møller-Plesset perturbation theory.
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| pubmed:affiliation |
National Institute of Advanced Industrial Science and Technology, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan. d.g.fedorov@aist.go.jp
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| pubmed:publicationType |
Journal Article
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