AMS-536 Molecular Modeling of Biological Molecules

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Please see for Rizzo Group Homepage (Research and Teaching)

Instructor Dr. Robert C. Rizzo [631-632-8519,]
Course No. AMS-536
Location/Time Math Tower, Room S235 (COMPUTER LAB next to SINC site), Mon/Wed 3:50PM - 5:10PM
Office Hours Anytime or by appointment, Room 1-101, Dept. of Applied Math & Statistics
Acknowledgments Chemical Computing Group for MOE software teaching licenses

Yan Yu and the Seawulf team
Pat Tonra for Mathlab support

GENERAL INFORMATION: AMS-536 is designed for students who wish to gain hands-on experience modeling biological molecules at the atomic level. In conjunction with the participants' interest, Molecular Mechanics, molecular dynamics, Monte Carlo, Docking (virtual screening), or Quantum Mechanics software packages will be used. Projects will include setup, execution, and analysis. Students will work on individual projects outside of class. Course participants will give presentations relevant to the simulations being performed and a final project report will be required. Familiarity with working in a Unix (Linux) environment is desirable.

DISABILITY SUPPORT SERVICES (DSS) STATEMENT: If you have a physical, psychological, medical, or learning disability that may impact your course work, please contact Disability Support Services (631) 632-6748 or They will determine with you what accommodations are necessary and appropriate. All information and documentation is confidential.

Students who require assistance during emergency evacuation are encouraged to discuss their needs with their professors and Disability Support Services. For procedures and information go to the following website:

ACADEMIC INTEGRITY STATEMENT: Each student must pursue his or her academic goals honestly and be personally accountable for all submitted work. Representing another person's work as your own is always wrong. Faculty are required to report any suspected instance of academic dishonesty to the Academic Judiciary. For more comprehensive information on academic integrity, including categories of academic dishonesty, please refer to the academic judiciary website at

CRITICAL INCIDENT MANAGEMENT: Stony Brook University expects students to respect the rights, privileges, and property of other people. Faculty are required to report to the Office of Judicial Affairs any disruptive behavior that interrupts their ability to teach, compromises the safety of the learning environment, and/or inhibits students' ability to learn.

LITERATURE: Hyperlinks and manuscripts accessed through Stony Brook University's electronic journal subscriptions are provided below for educational purposes only.

DISCLAIMER: Presentations may contain slides from a variety of online sources for educational and illustrative purposes only, and use here does not imply that the presenter is claiming that the contents are their own original work or research.

Course Schedules