1
|
|
2
|
Brooks B, Brooks C, MacKerell A, Nilsson L, Petrella R, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner A, Feig M, Fischer S, Gao J, Hodoscek M, Im W, Kuczera K, Lazaridis T, Ma J, Ovchinnikov V, Paci E, Pastor R, Post C, Pu J, Schaefer M, Tidor B, Venable RM, Woodcock HL, Wu X, Yang W, York D, Karplus M. CHARMM: the biomolecular simulation program. J Comput Chem 2009; 30:1545-614. [PMID: 19444816 PMCID: PMC2810661 DOI: 10.1002/jcc.21287] [Citation(s) in RCA: 6011] [Impact Index Per Article: 400.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecular simulation program. It has been developed over the last three decades with a primary focus on molecules of biological interest, including proteins, peptides, lipids, nucleic acids, carbohydrates, and small molecule ligands, as they occur in solution, crystals, and membrane environments. For the study of such systems, the program provides a large suite of computational tools that include numerous conformational and path sampling methods, free energy estimators, molecular minimization, dynamics, and analysis techniques, and model-building capabilities. The CHARMM program is applicable to problems involving a much broader class of many-particle systems. Calculations with CHARMM can be performed using a number of different energy functions and models, from mixed quantum mechanical-molecular mechanical force fields, to all-atom classical potential energy functions with explicit solvent and various boundary conditions, to implicit solvent and membrane models. The program has been ported to numerous platforms in both serial and parallel architectures. This article provides an overview of the program as it exists today with an emphasis on developments since the publication of the original CHARMM article in 1983.
Collapse
Affiliation(s)
- B.R. Brooks
- Laboratory of Computational Biology, National Heart, Lung, and
Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - C.L. Brooks
- Departments of Chemistry & Biophysics, University of
Michigan, Ann Arbor, MI 48109
| | - A.D. MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy,
University of Maryland, Baltimore, MD, 21201
| | - L. Nilsson
- Karolinska Institutet, Department of Biosciences and Nutrition,
SE-141 57, Huddinge, Sweden
| | - R.J. Petrella
- Department of Chemistry and Chemical Biology, Harvard University,
Cambridge, MA 02138
- Department of Medicine, Harvard Medical School, Boston, MA
02115
| | - B. Roux
- Department of Biochemistry and Molecular Biology, University of
Chicago, Gordon Center for Integrative Science, Chicago, IL 60637
| | - Y. Won
- Department of Chemistry, Hanyang University, Seoul
133–792 Korea
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - M. Karplus
- Department of Chemistry and Chemical Biology, Harvard University,
Cambridge, MA 02138
- Laboratoire de Chimie Biophysique, ISIS, Université de
Strasbourg, 67000 Strasbourg France
| |
Collapse
|
3
|
Peck SL. Simulation as experiment: a philosophical reassessment for biological modeling. Trends Ecol Evol 2007; 19:530-4. [PMID: 16701318 DOI: 10.1016/j.tree.2004.07.019] [Citation(s) in RCA: 175] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2003] [Revised: 07/19/2004] [Accepted: 07/29/2004] [Indexed: 11/22/2022]
Abstract
Some scientific modelers suggest that complex simulation models that mimic biological processes should have a limited place in ecological and evolutionary studies. However, complex simulation models can have a role that is different from that of simpler models that are designed to be fit to data. Simulation can be viewed as another kind of experimental system and should be analyzed as such. Here, I argue that current discussions in the philosophy of science and in the physical sciences fields about the use of simulation as an experimental system have important implications for biology, especially complex sciences such as evolution and ecology. Simulation models can be used to mimic complex systems, but unlike nature, can be manipulated in ways that would be impossible, too costly or unethical to do in natural systems. Simulation can add to theory development and testing, can offer hypotheses about the way the world works and can give guidance as to which data are most important to gather experimentally.
Collapse
Affiliation(s)
- Steven L Peck
- Department of Integrative Biology, Brigham Young University, Provo, UT 84602, USA.
| |
Collapse
|
4
|
Maggiora GM, Mao B, Chou KC, Narasimhan SL. Theoretical and empirical approaches to protein-structure prediction and analysis. METHODS OF BIOCHEMICAL ANALYSIS 2006; 35:1-86. [PMID: 2002769 DOI: 10.1002/9780470110560.ch1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
|
5
|
Simonson T, Wong CF, Brünger AT. Classical and Quantum Simulations of Tryptophan in Solution. J Phys Chem A 1997. [DOI: 10.1021/jp962810w] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Thomas Simonson
- Laboratoire de Biologie Structurale (C.N.R.S.), I.G.B.M.C., 1 rue Laurent Fries, 67404 Illkirch (C.U. de Strasbourg), France, Department of Physiology and Biophysics, Mount Sinai School of Medicine, Box 1218, New York, New York 10029-6574, and Howard Hughes Medical Institute, and Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06511
| | - Chung F. Wong
- Laboratoire de Biologie Structurale (C.N.R.S.), I.G.B.M.C., 1 rue Laurent Fries, 67404 Illkirch (C.U. de Strasbourg), France, Department of Physiology and Biophysics, Mount Sinai School of Medicine, Box 1218, New York, New York 10029-6574, and Howard Hughes Medical Institute, and Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06511
| | - Axel T. Brünger
- Laboratoire de Biologie Structurale (C.N.R.S.), I.G.B.M.C., 1 rue Laurent Fries, 67404 Illkirch (C.U. de Strasbourg), France, Department of Physiology and Biophysics, Mount Sinai School of Medicine, Box 1218, New York, New York 10029-6574, and Howard Hughes Medical Institute, and Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06511
| |
Collapse
|
6
|
Gilson MK, Given JA, Bush BL, McCammon JA. The statistical-thermodynamic basis for computation of binding affinities: a critical review. Biophys J 1997; 72:1047-69. [PMID: 9138555 PMCID: PMC1184492 DOI: 10.1016/s0006-3495(97)78756-3] [Citation(s) in RCA: 892] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Although the statistical thermodynamics of noncovalent binding has been considered in a number of theoretical papers, few methods of computing binding affinities are derived explicitly from this underlying theory. This has contributed to uncertainty and controversy in certain areas. This article therefore reviews and extends the connections of some important computational methods with the underlying statistical thermodynamics. A derivation of the standard free energy of binding forms the basis of this review. This derivation should be useful in formulating novel computational methods for predicting binding affinities. It also permits several important points to be established. For example, it is found that the double-annihilation method of computing binding energy does not yield the standard free energy of binding, but can be modified to yield this quantity. The derivation also makes it possible to define clearly the changes in translational, rotational, configurational, and solvent entropy upon binding. It is argued that molecular mass has a negligible effect upon the standard free energy of binding for biomolecular systems, and that the cratic entropy defined by Gurney is not a useful concept. In addition, the use of continuum models of the solvent in binding calculations is reviewed, and a formalism is presented for incorporating a limited number of solvent molecules explicitly.
Collapse
Affiliation(s)
- M K Gilson
- Center for Advanced Research in Biotechnology, National Institute of Standards and Technology, Rockville, Maryland 20850-3479, USA.
| | | | | | | |
Collapse
|
7
|
Zheng C, Makarov V, Wolynes PG. Statistical Survey of Transition States and Conformational Substates of the Sperm Whale Myoglobin−CO Reaction System. J Am Chem Soc 1996. [DOI: 10.1021/ja9523092] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chong Zheng
- Contribution from the Departments of Chemistry, Northern Illinois University, DeKalb, Illinois 60115, and University of Illinois, Urbana, Illinois 61801
| | - Vladimir Makarov
- Contribution from the Departments of Chemistry, Northern Illinois University, DeKalb, Illinois 60115, and University of Illinois, Urbana, Illinois 61801
| | - Peter G. Wolynes
- Contribution from the Departments of Chemistry, Northern Illinois University, DeKalb, Illinois 60115, and University of Illinois, Urbana, Illinois 61801
| |
Collapse
|
8
|
Gao J, Xia X. A priori evaluation of aqueous polarization effects through Monte Carlo QM-MM simulations. Science 1992; 258:631-5. [PMID: 1411573 DOI: 10.1126/science.1411573] [Citation(s) in RCA: 454] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A Monte Carlo quantum mechanical-molecular mechanical (QM-MM) simulation method was used to determine the contributions of the solvent polarization effect to the total interaction energies between solute and solvent for amino acid side chains and nucleotide bases in aqueous solution. In the present AM1-TIP3P approach, the solute molecule is characterized by valence electrons and nucleus cores with Hartree-Fock theory incorporating explicit solvent effects into the total Hamiltonian, while the solvent is approximated by the three-point charge TIP3P model. The polarization energy contributes 10 to 20 percent of the total electrostatic energy in these systems. The performance of the hybrid AM1-TIP3P model was further validated by consideration of bimolecular complexes with water and by computation of the free energies of solvation of organic molecules using statistical perturbation theory. Excellent agreement with ab initio 6-31G(d) results and experimental solvation free energies was obtained.
Collapse
Affiliation(s)
- J Gao
- Department of Chemistry, State University of New York, Buffalo 14214
| | | |
Collapse
|
9
|
Field MJ. A molecular dynamics simulation of photo-induced electron transfer in an organic donor—acceptor compound. Chem Phys Lett 1992. [DOI: 10.1016/0009-2614(92)85622-h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
10
|
Zheng C, McCammon J, Wolynes PG. Quantum simulations of conformation reorganization in the electron transfer reactions of tuna cytochrome c. Chem Phys 1991. [DOI: 10.1016/0301-0104(91)87070-c] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
11
|
|