2007 Spring Course Syllabus: AMS-536

Molecular Modeling of Biological Molecules

Spring 2007
Instructor: Dr. Robert C. Rizzo [631-632-9340, rizzo@ams.sunysb.edu]
Course: AMS-536 (3 Credits / 0 Audit) http://www.ams.sunysb.edu/~rizzo (go to Teaching)
When:   2:20AM-3:40PM, Monday and Wednesday, Math S235 (SINC site)
Office Hours:   Anytime or by appointment, Room 1-101, Dept. of Applied Math & Statistics
Hyperlinks accessed through Stony Brook University's electronic journal subscriptions are provided below for educational purposes only.


Final Project Guidelines and Sample Reports
Files and Links
Project Guidelines
Sample report project.example.dGhyd.pdf

Sample report



Unix Tutorial for Beginners http://www.ee.surrey.ac.uk/Teaching/Unix
Vi Text Editor Tutorial At linux prompt type "vimtutor" (without the quotes)
Molecular Mechanics Tutorial Colby College Molecular Mechanics Tutorial
MOE Tutorial see Help/Tutorials and Colby College MOE Tutorial
AMBER8 Tutorial AMBER8_intro.pdf
VMD Tutorial http://www.ks.uiuc.edu/Research/vmd/current/docs.html#tutorials
Software Links and Manuals
AMBER http://amber.scripps.edu/ (users manual here)
BOSS / MCPRO http://zarbi.chem.yale.edu/ (users manual here)
DOCK http://dock.compbio.ucsf.edu/ (users manual here)
MOE (Chemical Computing Group) http://www.chemcomp.com/ (see help menu for users manual)
VMD (visualization software) http://www.ks.uiuc.edu/Research/vmd/ (users manual here)
NCI (ligand database)
NIST (small molecule database) http://webbook.nist.gov/chemistry/
ZINC (ligand database) http://blaster.docking.org/zinc/
Project Notes
MC simulation of a pure liquid


Presentation Date
02/26/2007 Ricky, Jerry
02/28/2007 Christina, Alvin
03/05/2007 Jonathan, Diana
03/12/2007 Tony, Yukiji
03/14/2007 Shyam, Vadim
03/19/2007 Rose, Freda
03/21/2007 Trent, Liang
04/09/2007 Yan, Jerry
04/11/2007 Christina, Alvin
04/16/2007 Jonathan, Diana
04/18/2007 Tony, Yukiji
04/23/2007 Shyam, Vadim
04/25/2007 Rose, Freda
04/30/2007 Trent, Liang
05/02/2007 Yan, Ricky
If you have a physical, psychological, medical, or learning disability that may impact your course work, please contact Disability Support Services (631) 632-6748.  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: http://www.ehs.sunysb.edu and search Fire Safety and Evacuation and Disabilities.