University of Maryland Baltimore County

Fall Semester, 2005

Instructor: C. Allen Bush - Phone. 5-2506

e-mail: bush@umbc.edu

Prerequisites: Chem 301 (or Chem 303) and Chem 437 or equivalents.

This is an advanced 'Special Topics' course for which no text covers the material. Material will be placed on overnight reserve in the UMBC Library and copies of original papers will be distributed in class.

The only required book is 'Learning the unix operating system' by Peek, Todino and Strang (O'Reilly publ.)

Reserved books in UMBC library:

• ``Molecular Modeling: principles and applications'' by A.R. Leach Longman, 1996
• "Dynamics of Proteins and Nucleic Acids" by J. A. McCammon and S. C. Harvey., publ. Cambridge U. press, 1987.
• ``Physical Biochemistry'' by K. E. van Holde, W. C. Johnson and P. S. Ho publ. Prentice-Hall, 1998.
• Daan Frenkel (Editor) and Berend Smit (Editor) ``Understanding Molecular Simulation : From Algorithms to Applications'' Academic Press (1996)
• Molecular Mechanics across Chemistry'' by A.K. Rappe and C.J. Casewit 1997, University Science Books.
• CHARMm User's Guide and CHARMm Dictionary.
• Quanta User's Guide

website http://www.research.umbc.edu/ ~ bush/course/ch644/ch644.html

• The course will include a survey of theoretical methods for simulation of biopolymer conformation such as energy maps, energy minimization and molecular dynamics simulation. The basic physics behind the methods will be described including the parameterization of the potential energy functions and the influence of solvent. Applications will be described for proteins, nucleic acids and polysaccharides.
• The course will include practical details of the computer usage for molecular modeling calculations using the CHARMm code. You are expected to have an account on the Unix workstations of the UMBC academic computing service to carry out these assignments. You will be assigned projects involving various computational methods. Students will be expected to plan and carry out original projects of their own design in computer simulation of molecules. During laboratory periods, demonstrations of various computational examples will be given and students will be able to carry out exercises and ask questions about details of their execution.
• If you are not familiar with the Unix computing syntax and operations, consult the course website which has some links to tutorials and other introductory material. A number of more extensive books on Unix are on sale at the campus bookstore.
• Graduate students registered for Chem 644 will also be expected to prepare a brief seminar (20 mins) on a topic in biochemical molecular modeling to be selected from the current literature. Grades will be based on the quality of the presentation, which will be judged by all the students. These seminars will be held near the end of the semester.
• There will be a final exam which will be based on the course material and the topics covered in the student seminars. Course grade will be based on the computational homework assignments, the projects, seminar and final exam.