메뉴 건너뛰기




Volumn 111, Issue 9, 2007, Pages 2242-2254

Comparison of charge models for fixed-charge force fields: Small-molecule hydration free energies in explicit solvent

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL BONDS; COMPUTER SIMULATION; ELECTRIC CHARGE; FREE ENERGY; MATHEMATICAL MODELS; MOLECULAR MECHANICS;

EID: 33947397110     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp0667442     Document Type: Article
Times cited : (243)

References (61)
  • 23
    • 84906404377 scopus 로고    scopus 로고
    • Frisch, M. J, Trucks, G. W, Schlegel, H. B, Scuseria, G. E, Robb, M. A, Cheeseman, J. R, Montgomery, J. A, Jr, Vreven, T, Kudin, K. N, Burant, J. C, Millam, J. M, Iyengar, S. S, Tomasi, J, Barone, V, Mennucci, B, Cossi, M, Scalmani, G, Rega, N, Petersson, G. A, Nakatsuji, H, Hada, M, Ehara, M, Toyota, K, Fukuda, R, Hasegawa, J, Ishida, M, Nakajima, T, Honda, Y, Kitao, O, Nakai, H, Kiene, M, Li, X, Knox, J. E, Hratchian, H. P, Cross, J. B, Bakken, V, Adamo, C, Jaramillo, J, Gomperts, R, Stratmann, R. E, Yazyev, O, Austin, A. J, Cammi, R, Pomelli, C, Ochterski, J. W, Ayala, P. Y, Morokuma, K, Voth, G. A, Salvador, P, Dannenberg, J. J, Zakrzewski, V. G, Dapprich, S, Daniels, A. D, Strain, M. C, Farkas, O, Malick, D. K, Rabuck, A. D, Raghavachari, K, Foresman, J. B, Ortiz, J. V, Cui, Q, Baboul, A. G, Clifford, S, Cioslowski, J, Stefanov, B. B, Liu, G, Liashenko, A, Piskorz, P, Komaromi, I, Martin, R. L, Fox, D. J, Keit
    • Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A., Jr.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Kiene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian 03, revision C.02; Gaussian, Inc.: Wallingford, CT, 2004.
  • 39
    • 84906361158 scopus 로고    scopus 로고
    • Hawkins, G. D, Giesen, D. J, Lynch, G. C, Chambers, C. C, Rossi, I, Storer, J. W, Li, J, Zhu, T, Thompson, J. D, Winget, P, Lynch, B. J, Rinaldi, D, Liotard, D. A, Cramer, C. J, Truhlar, D. G. AMSOL, version 6.5.3; University of Minnesota: Minneapolis, MN, 1998
    • Hawkins, G. D.; Giesen, D. J.; Lynch, G. C.; Chambers, C. C.; Rossi, I.; Storer, J. W.; Li, J.; Zhu, T.; Thompson, J. D.; Winget, P.; Lynch, B. J.; Rinaldi, D.; Liotard, D. A.; Cramer, C. J.; Truhlar, D. G. AMSOL, version 6.5.3; University of Minnesota: Minneapolis, MN, 1998. http://comp.chem.umn. edu/amsol/.
  • 40
    • 84906404378 scopus 로고    scopus 로고
    • Case, D. A, Darden, T. A, Cheatham, T. E, III, Simmerling, C. L, Wang, J, Duke, R. E, Luo, R, Merz, K. M, Wang, B, Pearlman, D. A, Crowley, M, Brozell, S, Tsui, V; Gohlke, H, Mongan, J, Hornak, V, Cui, G, Beroza, P, Schafmeister, C, Caldwell, J. W, Ross, W. S, Kollman, P. A. AMBER, version 8; University of California: San Francisco, 2004
    • Case, D. A.; Darden, T. A.; Cheatham, T. E., III.; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Merz, K. M.; Wang, B.; Pearlman, D. A.; Crowley, M.; Brozell, S.; Tsui, V; Gohlke, H.; Mongan, J.; Hornak, V.; Cui, G.; Beroza, P.; Schafmeister, C.; Caldwell, J. W.; Ross, W. S.; Kollman, P. A. AMBER, version 8; University of California: San Francisco, 2004.
  • 41
    • 84906375702 scopus 로고    scopus 로고
    • The AMBER-to-GROMACS conversion script was originally written by Eric Sorin in the laboratory of Vijay Pande and modified and updated by the present authors. It is available online at
    • The AMBER-to-GROMACS conversion script was originally written by Eric Sorin in the laboratory of Vijay Pande and modified and updated by the present authors. It is available online at http://folding.stanford.edu/ffamber.
  • 54
    • 0011757586 scopus 로고    scopus 로고
    • Statistical analysis of simulations: Data correlations and error estimation
    • Grostendorst, J, Marx, D, Murmatsu, A, Eds, John von Neumann Institute for Computing: Julich, Germany
    • Janke, W. Statistical analysis of simulations: Data correlations and error estimation. In Quantum Simulations of Complex Many-Body Systems: From Theory to Algorithms; Grostendorst, J.; Marx, D.; Murmatsu, A., Eds.; John von Neumann Institute for Computing: Julich, Germany, 2002.
    • (2002) Quantum Simulations of Complex Many-Body Systems: From Theory to Algorithms
    • Janke, W.1
  • 60
    • 84906404375 scopus 로고    scopus 로고
    • The AMBER 8 version of ANTECHAMBER omits improper torsions for some molecules for which improper torsions are included in some later versions of ANTECHAMBER. Hence, there may be some systematic differences in the parameters generated with this version of ANTECHAMBER compared to those generated with some later versions. These improper torsions typically seem to involve aromatic hydrogens and carbons in molecules such as phenol and o-cresol and enforce hydrogen planarity. We have tested the robustness of our results to these parameters by repeating our calculations for several molecules (phenol and o-cresol) with parameters generated using ANTECHAMBER version 1.2.4 and found that any differences in computed hydration free energies were within the statistical uncertainty; hence we have not further examined this issue here
    • The AMBER 8 version of ANTECHAMBER omits improper torsions for some molecules for which improper torsions are included in some later versions of ANTECHAMBER. Hence, there may be some systematic differences in the parameters generated with this version of ANTECHAMBER compared to those generated with some later versions. These improper torsions typically seem to involve aromatic hydrogens and carbons in molecules such as phenol and o-cresol and enforce hydrogen planarity. We have tested the robustness of our results to these parameters by repeating our calculations for several molecules (phenol and o-cresol) with parameters generated using ANTECHAMBER version 1.2.4 and found that any differences in computed hydration free energies were within the statistical uncertainty; hence we have not further examined this issue here.
  • 61
    • 84906361157 scopus 로고    scopus 로고
    • 43 in the data and thus also represents an underestimate of the true uncertainty.
    • 43 in the data and thus also represents an underestimate of the true uncertainty.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.