CONGEN

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A disclaimer is necessary here. Since CONGEN is under continuous development, and because we do not have continuous access to all these machines, "ported" means that it was successfully compiled and executed on those machines at some point prior to the current release. Changes made to the code after the test may not compile, but it should be a simple matter to correct any problems.

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They can also be constructed by the internal coordinate commands, see section The Internal Coordinate Commands, but HBUILD is more intelligent than the internal coordinate commands.

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R. E. Bruccoleri, "Grid Positioning Independence and the Reduction of Self-Energy in the Solution of the Poisson-Boltzmann Equation", J. Comput. Chem. 14, 1417-1422 (1993).

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Stephen C. Harvey, "Treatment of Electrostatic Effects in Macromolecular Modeling", Proteins: Struct. Funct. Gen. 5, 78-92 (1989)

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J. Warwicker and H. C. Watson, "Calculation of the Electric Potential in the Active Site Cleft Due to alpha-Helix Dipoles", J. Mol. Biol. 157, 671-679, (1982).

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Malcolm E. Davis and J. Andrew McCammon, "Solving the Finite Difference Linearized Poisson-Boltzmann Equation: A Comparison of Relaxation and Conjugate Gradient Methods", J. Comput. Chem, 10, 386-391, (1989).

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Anthony Nicholls and Barry Honig, "A Rapid Finite Difference Algorithm, Utilizing Successive Over-Relaxation to Solve the Poisson-Boltzmann Equation", J. Comput. Chem 12, 435-445, (1991).

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Malcolm E. Davis and J. Andrew McCammon, "Electrostatics in Biomolecular Structure and Dynamics", Chem. Rev. 90 509-521 (1990).

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W. H. Press and B. P. Flannery and S. A. Teukolsky and W. T. Vetterling, Numerical Recipes: The Art of Scientific Computing, Cambridge University Press, Cambridge, 1986, pp. 652-659.

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This is suggested by a paper by T. Simonson and D. Perahia, "Internal and interfacial dielectric properties of cytochrome c from molecular dynamics in aqueous solution. Proc. Natl. Acad. Sci. USA 92, 1082-1086 (1995).

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M. Karplus, J. Chem. Phys. 30, 11-15 (1959).

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M. Karplus, J. Am. Chem. Soc. 85, 2870-2871 (1963).

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For example, the van der Waals avoidance in the sidechain construction will adjust a chi angle selection until a close contact is avoided. Also, the chain closure procedure generates torsion angles over the complete domain of angles. In addtion, backbone and sidechain degrees of freedom can construct atoms using fixed torsion angles.

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B. Lee and F. M. Richards, J. Mol. Biol., 55, 379 (1971)

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J.L. Pascual-Ahuir, E. Silla and I. Tunon, QCPE 554, 1993

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J. L. Pascual-Ahuir and E. Silla GEPOL: An improved description of molecular surfaces. I. Building the spherical surface set. J. Comput. Chem., 11 (1990) 1047-1060.

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E. Silla, I. Tunon and J. L. Pascual-Ahuir GEPOL: An improved description of molecular surfaces. II. Computing the molecular area and volume. J. Comput. Chem., 12 (1991) 1077-1088.

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J. L. Pascual-Ahuir, I Tunon and E. Silla GEPOL: An improved description of molecular surfaces. III. A New algorithm for the computation of the Solvent-Excluding Surface. To be submitted to J. Comput. Chem. during 1993

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You can use the homology program, see section homology -- Simple Homology Program, to find the homology between two sequences.

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R. A. Wagner and M. J. Fischer, "The String To String Correction Problem", J. Association of Computing Machinery 21, 168-173 (1974).

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as of Irix 3.3

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Gaussian 92, Revision C, M. J. Frisch, G. W. Trucks, M. Head-Gordon, P. M. W. Gill, M. W. Wong, J. B. Foresman, B. G. Johnson, H. B. Schlegel, M. A. Robb, E. S. Replogle, R. Gomperts, J. L. Andres, K. Raghavachari, J. S. Binkley, C. Gonzalez, R. L. Martin, D. J. Fox, D. J. Defrees, J. Baker, J. J. P. Stewart, and J. A. Pople, Gaussian, Inc., Pittsburgh PA, 1992.

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D.E. Williams, Quantum Chemistry Program Exchange, Program 568; PDM88 (which includes PDGRID)

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D. E. Williams, "Representation of the Molecular Electrostatic Potential by Atomic Multipole and Bond Dipole Models", J. Comput. Chem. 9, 745-763 (1988).

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The program, PDM88, is obsolete. Although it serves the need for a charge calculation in CONGEN, the newer version has more features for those users interested in exploring charge calculations. For further information please contact Dr. Donald E. Williams, Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, USA, Tel: (502)588-5975, Fax: (502)588-8149, E-mail: dewill01@ulkyvx.bitnet.

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U. C. Singh and P. A. Kollman, J. Comput. Chem., 5, 129 (1984).

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B. H. Besler, K. M. Merz, and P. A Kollman, J. Comput. Chem., 11, 431 (1990).

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L. E. Chirlian and M. M. Francl, J. Comput. Chem., 8, 894 (1987).

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C. M. Breneman and K. B. Wiberg, J. Comput. Chem., 11, 361 (1990).

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See S.D. Conte and C. de Boor, Elementary Numerical Analysis, an Algorithmic Approach, McGraw-Hill Book Company, New York 1972, p. 282

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J.L. Pascual-Ahuir, E. Silla and I. Tunon, QCPE 554, 1993

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J. L. Pascual-Ahuir and E. Silla GEPOL: An improved description of molecular surfaces. I. Building the spherical surface set. J. Comput. Chem., 11 (1990) 1047-1060.

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E. Silla, I. Tunon, and J. L. Pascual-Ahuir, GEPOL: An improved description of molecular surfaces. II. Computing the molecular area and volume. J. Comput. Chem., 12 (1991) 1077-1088.

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J. L. Pascual-Ahuir, I. Tunon and E. Silla GEPOL: An improved description of molecular surfaces. III. A New algorithm for the computation of the Solvent-Excluding Surface. J. Comput. Chem. 15 (1994) 1127-1138.

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I. Tunon, E. Silla, and J. L. Pascual-Ahuir, Molecular surface area and hydrophobic effect. Prot. Eng. 5 (1992) 715-716.

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The installation script is Copyright (C) 1984, 1985,1986, 1987, 1988, 1989, 1990, 1991 by the Massachusetts Institute of Technology.

Permission to use, copy, modify, distribute, and sell this software and its documentation for any purpose is hereby granted without fee, provided that the above copyright notice appear in all copies and that both that copyright notice and this permission notice appear in supporting documentation, and that the name of MIT not be used in advertising or publicity pertaining to distribution of the software without specific, written prior permission. MIT makes no representations about the suitability of this software for any purpose. It is provided "as is" without express or implied warranty.

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Scott J. Weiner, Peter A. Kollman, Dzung T. Nguyen and David A. Case, "An All Atom Force Field for Simulations of Proteins and Nucleic Acids", J. Comput. Chem 7, 230-252 (1986)

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Scott J. Weiner, Peter A. Kollman, Dzung T. Nguyen and David A. Case, "An All Atom Force Field for Simulations of Proteins and Nucleic Acids", J. Comput. Chem 7, 230-252 (1986)

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Wendy D. Cornell, Piotr Cieplak, Christopher I. Bayly, Ian R. Gould, Kenneth M. Merz, Jr., David M. Furguson, David C. Spellmeyer, Thomas Fox, James W. Caldwell and Peter A. Kollman, "A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules", J. Am. Chem. Soc. 117, 5179-5197 (1995)