AFMM: A molecular mechanics force field vibrational parametrization program

Computer Physics Communications

Volumn 167, Issue 1, 2005, Pages 34-42

  Vaiana, A C ^a   Cournia, Z ^a   Costescu, I B ^a   Smith, J C ^a  

^a UNIVERSITY OF HEIDELBERG   (Germany)

Author keywords

Force field parametrization; Molecular mechanics; Normal mode analysis; Parameter optimization

Indexed keywords

ALGORITHMS; APPROXIMATION THEORY; COMPUTER SIMULATION; DEGREES OF FREEDOM (MECHANICS); EIGENVALUES AND EIGENFUNCTIONS; HARMONIC ANALYSIS; MATHEMATICAL MODELS; MONTE CARLO METHODS; OPTIMIZATION; PARAMETER ESTIMATION; POTENTIAL ENERGY;

AUTOMATED FREQUENCY MATCHING METHOD (AFMM); FORCE FIELD PARAMETRIZATION; MOLECULAR MECHANICS (MM); NORMAL MODE ANALYSIS; PARAMETER OPTIMIZATION; TORSION ANGLE; VIBRATIONAL PARAMETRIZATION;

MOLECULAR DYNAMICS;

EID: 14844330742     PISSN: 00104655     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cpc.2004.12.005     Document Type: Article

References (11)

1. B.R. Brooks, O. Bruccoleri, B.D. Olafson, D.J. States, S. Swaminathan, and M. Karplus CHARMM: A program for macromolecular energy, minimization and dynamics calculations J. Comp. Biol. 4 1983 187
2. P. Norrby, and T. Liljefors Automated molecular mechanics parametrization with simultaneous utilization of experimental and quantum mechanical data J. Comp. Chem. 10 1998 1146
3. A. Hopfinger, and R. Pearlstein Molecular mechanics force-field parameterization procedures J. Comp. Chem. 5 1984 486
4. G. Schaftenaar, and J. Noordik Molden: a pre- and post-processing program for molecular and electronic structures J. Comput.-Aided Mol. Design 14 2000 123 134
5. M.J. Frisch, G.W. Trucks, H.B. Schlegel, P.M.W. Gill, B.G. Johnson, M.A. Robb, J.R. Cheeseman, T. Keith, G.A. Petersson, J.A. Montgomery, K. Raghavachari, M.A. Al-Laham, V.G. Zakrzewski, J.V. Ortiz, J.B. Foresman, J. Cioslowski, B.B. Stefanov, A. Nanayakkara, M. Challacombe, G.Y. Peng, P.Y. Ayala, W. Chen, M.W. Wong, J.L. Andres, E.S. Replogle, R. Gomperts, R.L. Martin, D.J. Fox, J.S. Binkley, D.J. Defrees, J. Baker, J.P. Stewart, M. Head-Gordon, C. Gonzalez, and J.A. Pople Gaussian 94, Revision E.1 1995 Gaussian, Inc. Pittsburgh, PA
6. M.J. Frisch, G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, J.R. Cheeseman, V.G. Zakrzewski, J.J.A. Montgomery, R.E. Stratmann, J.C. Burant, S. Dapprich, J.M. Millam, A.D. Daniels, K.N. Kudin, M.C. Strain, O. Farkas, J. Tomasi, V. Barone, M. Cossi, R. Cammi, B. Mennucci, C. Pomelli, C. Adamo, S. Clifford, J. Ochterski, G.A. Petersson, P.Y. Ayala, Q. Cui, K. Morokuma, D.K. Malick, A.D. Rabuck, K. Raghavachari, J.B. Foresman, J. Cioslowski, J.V. Ortiz, A.G. Baboul, B.B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. Gomperts, R.L. Martin, D.J. Fox, T. Keith, M.A. Al-Laham, C.Y. Peng, A. Nanayakkara, M. Challacombe, P.M.W. Gill, B. Johnson, W. Chen, M.W. Wong, J.L. Andres, C. Gonzalez, M. Head-Gordon, E.S. Replogle, and J.A. Pople Gaussian 98, Revision A.9 1998 Gaussian, Inc. Pittsburgh, PA
7. R.J. Harrison, J.A. Nichols, T.P. Straatsma, M. Dupuis, E.J. Bylaska, G.I. Fann, T.L. Windus, E. Apra, J. Anchell, D. Bernholdt, P. Borowski, T. Clark, D. Clerc, H. Dachsel, B. de Jong, M. Deegan, K. Dyall, D. Elwood, H. Fruchtl, E. Glendenning, M. Gutowski, A. Hess, J. Jaffe, B. Johnson, J. Ju, R. Kendall, R. Kobayashi, R. Kutteh, Z. Lin, R. Littlefield, X. Long, B. Meng, J. Nieplocha, S. Niu, M. Rosing, G. Sandrone, M. Stave, H. Taylor, G. Thomas, J. van Lenthe, K. Wolinski, A. Wong, Z. Zhang, NWChem, A Computational Chemistry Package for Parallel Computers, Version 4.0.1, Pacific Northwest National Laboratory, Richland, Washington, USA
8. G. te Velde, R.M. Bickelhaupt, E.J. Baerends, C.F. Guerra, S.J.A. van Gisbergen, J.G. Snijders, and T. Ziegler Chemistry with ADF J. Comp. Chem. 22 2001 931
9. J. Foresman, and A. Frisch Exploring Chemistry with Electronic Structure Methods second ed. 1993 Gaussian, Inc. Pittsburgh, PA
10. A. Vaiana, A. Schulz, J. Worfrum, M. Sauer, and J. Smith Molecular mechanics force field parametrization of the fluorescent probe rhodamine 6G using automated frequency matching J. Comp. Chem. 24 2002 632
11. Z. Cournia, A. Vaiana, J.C. Smith, and G.M. Ullmann Derivation of a molecular mechanics force field for cholesterol Pure Appl. Chem. 76 1 2004 189