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Temperature Dependency on Conformational Sampling of 12-Crown-4 by Simulated Annealing
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  • Journal title : Journal of the Chosun Natural Science
  • Volume 6, Issue 1,  2013, pp.8-11
  • Publisher : The Research Institute of Chosun Natural Science
  • DOI : 10.13160/ricns.2013.6.1.008
 Title & Authors
Temperature Dependency on Conformational Sampling of 12-Crown-4 by Simulated Annealing
Gadhe, Changdev G.; Cho, Seung Joo;
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 Abstract
In this manuscript, we report a protocol to determine most of the lowest energy conformations from the ensemble of conformations. 12-crown-4 was taken as study compound to get the most of energy minima conformations. Molecular dynamic (MD) simulation for 1 nanosecond (ns) was performed at 300, 500, 700, 900 and 1100 K temperature. At particular interval conformations were sampled. Then Gaussian program was used to minimize compounds using PM6 energy levels. Duplicates were removed by checking energy as well as mirror image conformations, and only unique conformations were retained for the next level minimization. It was observed that upto certain increment in temperature the number of unique conformations were increased, but afterword it decreased.
 Keywords
Molecular Dynamics;Simulated Annealing;Conformational Sampling;PM6;;
 Language
English
 Cited by
 References
1.
R. Elber and M. Karplus, "Enhanced sampling in molecular dynamics: use of the time-dependent Hartree approximation for a simulation of carbon monoxide diffusion through myoglobin", J. Am. Chem. Soc., Vol. 112, pp. 1961-1975, 1990.

2.
A. E. Garcia and K.Y. Sanbonmatsu, "Exploring the energy landscape of a beta hairpin in explicit solvent", Proteins, Vol. 42, pp. 345-354, 2001. crossref(new window)

3.
K. Tai, "Conformational sampling for the impatient", Biophys. Chem., Vol. 107, pp. 213-220, 2004. crossref(new window)

4.
R. E. Bruccoleri and M. Karplus, "Prediction of the folding of short polypeptide segments by uniform conformational sampling", Biopolymers, Vol. 26, pp. 137-168, 1987. crossref(new window)

5.
M. Saunders, "Stochastic exploration of molecular mechanics energy surface: hunting for the global minimum", J. Am. Chem. Soc., Vol. 109, pp. 3150-3152, 1987. crossref(new window)

6.
D. M. Ferguson and D. J. Raber, "A new approach to probing conformational space with molecular mechanics: random incremental pulse search", J. Am. Chem. Soc., Vol. 111, pp. 4371-4378, 1989. crossref(new window)

7.
Z. Q. Li and H. A. Scheraga, "Monte-carlo-minimi-zation approach to the multiple-minima problem in protein folding", Proc. Natl. Acad. Sci. U. S. A. Vol. 84, pp. 6611-6615, 1987. crossref(new window)

8.
S. H. R. SYBYL8.1; Tripos Inc., St. Louis, MO 63144 USA (2008).

9.
D. A. Case, T. A. Darden, T. E. Cheatham, III, C. L. Simmerling, J. Wang, R. E. Duke, R. Luo, R. C. Walker, W. Zhang, K. M. Merz, B. Roberts, S. Hayik, A. Roitberg, G. Seabra, J. Swails, A. W. Goetz, I. Kolossvary, K. F. Wong, F. Paesani, J. Vanicek, R. M. Wolf, J. Liu, X. Wu, S. R. Brozell, T. Steinbrecher, H. Gohlke, Q. Cai, X. Ye, J. Wang, M.-J. Hsieh, G. Cui, D. R. Roe, D. H. Mathews, M. G. Seetin, R. Salomon-Ferrer, C. Sagui, V. Babin, T. Luchko, S. Gusarov, A. Kovalenko, and P. A. Kollman, AMBER 12, University of California, San Francisco (2012).

10.
A. Jakalian, B. L. Bush, B. D. Jack, and C. I. Bayly, "Fast, efficient generation of high-quality atomic charges. AM1-BCC Model: I. Method", J. Comp. Chem., Vol. 21, pp. 132-146, 2000. crossref(new window)

11.
J. Wang, R. M. Wolf, J. W. Caldwell, P. A. Kollman, and D. A. Case, "Development and testing of a general amber force field", J. Comp. Chem., Vol. 25, pp. 1157-1173, 2004. crossref(new window)

12.
S. J. Cho, "Meaning and definition of partial charge", J. Chosun Natural Sci., Vol. 3, pp. 231-236, 2010.

13.
S. J. Cho, "Calculation and application of partial charge". J. Chosun Natural Sci., Vol. 3, pp. 226-230, 2010.