New Parameterization of the Cornell et al. Empirical Force Field Covering Amino Group Nonplanarity in Nucleic Acid Bases

Journal of Computational Chemistry

Volumn 24, Issue 15, 2003, Pages 1891-1902

  Ryjáček, Filip ^a   Kubař, Tomáš ^a   Hobza, Pavel ^a  

^a J HEYROVSKÝ INSTITUTE OF PHYSICAL CHEMISTRY   (Czech Republic)

Author keywords

Cornell et al. potential; Correlated ab initio calculations; Force field parameterization; Nonplanar amino group

Indexed keywords

CHEMICAL BONDS; MOLECULAR ORIENTATION; NUCLEIC ACIDS; POTENTIAL ENERGY;

FORCE FIELD PARAMETERIZATION;

AMINO ACIDS;

ADENINE; CYTOSINE; GUANINE; NUCLEIC ACID;

ARTICLE; BASE PAIRING; BINDING SITE; CHEMISTRY; HYDROGEN BOND; PHYSICAL CHEMISTRY; QUANTUM THEORY; THEORETICAL MODEL;

ADENINE; BASE PAIRING; BINDING SITES; CHEMISTRY, PHYSICAL; CYTOSINE; GUANINE; HYDROGEN BONDING; MODELS, THEORETICAL; NUCLEIC ACIDS; QUANTUM THEORY;

EID: 0142219440     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/jcc.10352     Document Type: Article

References (19)

1. Luisi, B.; Orozco, M.; Šponer, J.; Luque, F. J.; Shakked, Z. J Mol Biol 1998, 279, 1123.
2. Šponer, J.; Florián, J.; Hobza, P.; Leszczynski, J. J Biomol Struct Dynam 1996, 13, 827.
3. Kydd, R. A.; Krueger, P. J. J Chem Phys 1978, 69, 827.
4. Bludský, O.; Šponer, J.; Leszczynski, J.; Špirko, V.; Hobza, P. J Chem Phys 1996, 105, 11042.
5. Nir, E.; Janzen, Ch.; Imhof, P.; Kleinermanns, K.; de Vries, M. S. Phys Chem Chem Phys 2002, 4, 740.
6. Hobza, P.; Špirko, V. Phys Chem Chem Phys 2003, 5, 1290.
7. Šponer, J.; Hobza, P. J Phys Chem 1994, 98, 3161.
8. Šponer, J.; Hobza, P. Theochem 1994, 304, 35.
9. Šponer, J.; Leszczynski, J.; Hobza, P. J Biomol Struct Dynam 1996, 14, 117.
10. Pearlman, D. A.; Case, D. A.; Caldwell, J. W.; Ross, W. S.; Cheatham, T. E., III; Ferguson, D. M.; Seibel, G. L.; Singh, U. C.; Weiner, P. K.; Kollman P. A. AMBER 4.1, University of California, San Francisco, 1995.
11. MacKerell, A. D.; Bashford, D.; Bellott, M.; Dunbrack, R. L.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D. ; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E.; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. J Phys Chem B 1998, 102, 3586.
12. Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. J Am Chem Soc 1996, 118, 1125.
13. Cornell, W. D.; Cieplak, P.; Bayly C. I.; Gould, I. R.; Merz, K. M., Jr. ; Ferguson, D. M.; Spellmeyer, D. C., Fox, T., Caldwell, J. W.; Kollman P. A. J Am Chem Soc 1995, 117, 5197.
14. Feyereisen, M.; Fitzgerald, G.; Komornicki, A. Chem Phys Lett 1993, 208, 359.
15. Jurečka, P.; Nachtigall, P.; Hobza, P. Phys Chem Chem Phys 2001, 3, 4578.
16. Ahlrichs, R.; Bär, M.; Häser, M.; Horn, H.; Kölmel, C. Chem Phys Lett 1989, 162, 165.
17. Ponder, J. W. TINKER - Software Tools for Molecular Design, Version 3.9; Washington University School of Medicine, Saint Louis, MO, 2001.
18. Hobza, P.; Sandorfy, C. J Am Chem Soc 1987, 109, 1302.
19. Šponer, J.; Leszczynski, J.; Hobza, P. J Phys Chem 1996, 100, 1965.