TR 8:30-9:50, 225 Fraser + computer lab

The course will consist of three parts: a "theoretical" lecture, a laboratory lecture and a computer laboratory. The lectures will be held in class. The computer laboratory part will be performed individually or in small groups on SGI computers at several sites on campus. The instructor and/or other qualified personnel will be available for consultation during laboratory hours and at other times as needed. The goal of the course is to introduce students to computing and molecular modeling techniques so that they will be able to perform standard simulation tasks as part of their research. There is no official textbook; some useful references are given below. There will be no partial or final exams. The evaluation of performance will be based on laboratory reports, consisting of descriptions of methods, goals and results from the computer laboratory exercises performed during the semester. The whole class is organized around a central Web site. This site will contain all course materials : theoretical and laboratory lecture notes, tutorials for major software, manuals for computer laboratory exercises, modeling case studies as well as a mini-manual for UNIX.

1. Molecular mechanics
   • Describing molecules
   • Force fields : intra-- and intermolecular terms
   • Algorithms : energy evaluation \& minimization, conformational search, constraints, molecular vibrations
2. Molecular dynamics
   • Basic algorithms
   • Trajectory analysis
   • Applications
   • Special algorithms -- boundaries, constraints, free energy, etc.
3. Special topics. Limitations and future trends.

1. Introduction to UNIX, computer workstations, networking and the WWW
2. BIOLAB: Introduction to modeling software
3. QUANTA/CHARMM : describing molecules
4. The Brookhaven Protein Data Bank
5. QUANTA/CHARMM : structural and energetic dictionaries
6. QUANTA/CHARMM : calculating energy
7. QUANTA/CHARMM : energy minimization
8. QUANTA/CHARMM : molecular vibrations
9. QUANTA/CHARMM : manipulating molecules
10. Conformational search
11. CHARMM : molecular dynamics
12. CHARMM : solvation
13. Optional: Special topics depending on interest of students and available time (e.g. GAUSSIAN, computational spectroscopy, data analysis, Mathematica, ...)

1. Setting up computer accounts, lab groups and workstations (Week 1)
2. BIOLAB \#1 : Introduction to UNIX; PDB \& Kinemages (Week 2)
3. BIOLAB \#2 : RasMol and MolScript (Week 3)
4. BIOLAB \#3 : Creating molecular graphics (Week 4)
5. Introduction to QUANTA and CHARMM (Week 5)
6. Molecular energy surfaces: torsions and H-bonds (Week 6)
7. Normal mode analysis : water (Week 7)
8. Conformational search : energy minimization (Week 8)
9. Conformational search : molecular dynamics (Week 9)
10. MD simulation of a small protein : BPTI in vacuum (Week 10)
11. MD simulation of a solvated peptide (Week 11)
12. Creating Web-based educational material (Weeks 12--13)
13. Individual student-generated projects (Weeks 14--15).

A. R. Leach, Molecular Modeling. Principles and Applications Addison Wesley Longman, 1996.

M. Karplus, G.A. Petsko, Molecular dynamics simulations in biology, Nature,347,631--639 (1990).

W.F. van Gunsteren and H.J.C. Berendsen, Computer Simulations of Molecular Dynamics: Methodology, Applications and Perspectives in Chemistry, Angew. Chem. Int. Ed. Engl., 29, 992--1023, 1990.

C.L. Brooks III, M. Karplus, B.M. Pettitt, Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics, John Wiley and Sons, New York, 1988.

J.A. McCammon and S.C. Harvey,Dynamics of Proteins and Nucleic Acids, Cambridge University Press, 1988.

G. Todino, J. Strang and J. Peek, Learning the UNIX operating system, 3rd Ed, O'Reilly \& Associates, 1993.

J. M. Haile, Molecular Dynamics Simulation. Elementary Methods, John Wiley and Sons, New York, 1992.

M. P. Allen and B. J.Tildesley, Computer Simulations of Liquids, Clarendon, Oxford, 1987.

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