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Simulation of the hydration structure of glycyl-alanine
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Liang, T. and Walsh, T. R. (2007) Simulation of the hydration structure of glycyl-alanine. In: 3rd International Conference on Foundations of Molecular Modeling and Simulation (FOMMS), Blaine, WA, July 09-14, 2006. Published in: Molecular Simulation, Vol.33 (No.4-5). pp. 337-342. doi:10.1080/08927020601155378 ISSN 0892-7022.
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Official URL: http://dx.doi.org/10.1080/08927020601155378
Abstract
Molecular dynamics (MD) simulations studies have been performed on the aqueous solvation of the dipeptide glycyl-alanine (GA) using classical force-fields AMBER (J. Wang, P. Cieplak, P. A. Kollman, J. Comp. Chem. 21, 1049 (2000)) and CHARMM (N. Foloppe, A. D. MacKerell, J. Comp. Chem. 21, 86 (2000)), and the polarizable - force-field AMOEBAPRO (P. Ren, J. W. Ponder, J. Comp. Chem. 23, 1497 (2002), P. Ren, J. W. Ponder, J. Phys. Chem. B. 107, 5933 (2003)). Radial distribution functions and hydration numbers are calculated and compared with the data from Car-Parrinello molecular dynamics (CPMD) and experiments. Our results show all three force-fields can reproduce most of the features of the hydration structure of dipeptide GA. It is also found that AMBER and CHARMM force-fields can describe an averaged chemical environment, while AMOEBAPRO force-field has the capability of capturing the changes in the local environment caused by conformational transitions.
Item Type: | Conference Item (UNSPECIFIED) | ||||
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Subjects: | Q Science > QD Chemistry Q Science > QC Physics |
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Divisions: | Faculty of Science, Engineering and Medicine > Science > Chemistry | ||||
Journal or Publication Title: | Molecular Simulation | ||||
Publisher: | Taylor & Francis Inc. | ||||
ISSN: | 0892-7022 | ||||
Official Date: | 15 April 2007 | ||||
Dates: |
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Volume: | Vol.33 | ||||
Number: | No.4-5 | ||||
Number of Pages: | 6 | ||||
Page Range: | pp. 337-342 | ||||
DOI: | 10.1080/08927020601155378 | ||||
Status: | Not Peer Reviewed | ||||
Publication Status: | Published | ||||
Access rights to Published version: | Restricted or Subscription Access | ||||
Title of Event: | 3rd International Conference on Foundations of Molecular Modeling and Simulation (FOMMS) | ||||
Type of Event: | Conference | ||||
Location of Event: | Blaine, WA | ||||
Date(s) of Event: | July 09-14, 2006 |
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