boss46 - BOSS, Version 4.6 Biochemical and Organic...

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BOSS, Version 4.6 Biochemical and Organic Simulation System User’s Manual for UNIX, Linux, and Windows William L. Jorgensen Department of Chemistry, Yale University P. O. Box 208107 New Haven, Connecticut 06520-8107 Phone: (203) 432-6278 Fax: (203) 432-6299 Internet: william.jorgensen@yale.edu January 2004
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Contents Page I n t r o d u c t i o n 4 1 Can’t Wait to Start – Use the x Scripts 6 2 Statistical Mechanics Simulation – Theory 6 3 Energy and Free Energy Evaluation 7 4 N e w F e a t u r e s 9 5 O p e r a t i n g S y s t e m s 1 4 6 I n s t a l l a t i o n 1 4 7 F i l e s 1 4 8 Command or bat File Input 16 9 Parameter File Input 18 10 Z-matrix File Input 26 10.1 Atom Input 29 10.2 Geometry Variations 29 10.3 Bond Length Variations 29 10.4 Additional Bonds 30 10.5 Harmonic Restraints 30 10.6 Bond Angle Variations 30 10.7 Additional Bond Angles 31 10.8 Dihedral Angle Variations 31 10.9 Additional Dihedral Angles 33 10.10 Domain Definitions 34 10.11 Conformational Searching 34 10.12 Sample Z-matrix 34 10.13 Z-matrix Input for Custom Solvents 35 11 PDB Input 37 12 Coordinate Input in Mind Format and Reaction Path Following 38 13 Pure Liquid Simulations 39 1 4 C l u s t e r S i m u l a t i o n s 3 9 2
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15 Solventless and Molecular Mechanics Calculations 40 15.1 Continuum Simulations 40 15.2 Energy Minimizations 41 15.3 Dihedral Angle Driving 42 15.4 Potential Surface Scanning 42 15.5 Normal Coordinate Analysis 43 15.6 Conformational Searching 45 16 Available Solvent Boxes 48 17 Ewald Summation for Long-Range Electrostatics 50 18 Test Jobs 51 1 9 O u t p u t 5 6 19.1 Some Variable Definitions 58 20 Contents of the Distribution Files 59 21 Appendix – No. of Molecules for Binary Solvent Mixtures 61 22 Appendix - OPLS All-Atom Parameters 62 3
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Biochemical and Organic Simulation System Introduction The BOSS program performs (a) Monte Carlo (MC) statistical mechanics simulations for solutions of zero to 25 solute molecules in a periodic solvent box, in a solvent cluster, or in a dielectric continuum including the gas phase, and (b) standard energy minimizations, normal mode analysis, and conformational searching . The energetics are represented with the OPLS force fields or the AM1, PM3, PDDG/PM3 and PDDG/MNDO semiempirical molecular orbital methods. Besides the quantitative structural and energetic results, other quantities are computed including dipole moments, CM1 and CM3 atomic charges, solvent accessible surface areas, and hydrogen-bond counts that are valuable for many applications such as structure-activity relations . Some important features are: 1. For the Monte Carlo simulations, the NPT ensemble is employed, though NVT simulations can also be performed by not allowing volume changes. 2. Preferential sampling is used whereby the solutes and nearby solvent molecules are moved more frequently than distant solvent molecules. The biasing is based on 1 / ( r 2 + wkc ) where wkc is a constant. See J. Phys. Chem. 87 , 5311-5312 (1983).
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boss46 - BOSS, Version 4.6 Biochemical and Organic...

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