2010 AMBER Tutorial with Biotin and Streptavidin

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What is AMBER?

Amber - Assisted Model Building with Energy Refinement - is a suite of about 50 programs that can be used to simulate, and analyze macromolecular systems such as proteins dissolved in water at physiological conditions. Amber10, the current version (Amber11 soon to be released) of Amber is extremely advanced, powerful and fast. PMEMD, particle mesh Ewald (boundary condition treatment / parallelized code) can churn out 314 ps/day of data for the system dihydrofolate reductase (159 residue protein) in TIP3P water (23,558 total atoms).

Quick Tips

The Amber 10 Manual is the primary resource when trying to learn what variables and keywords mean and what they do. Using Adobe Acrobat to view the file, you can simply search the document for keywords, which saves much time.

There is a mailing list you could sign-up for, as an additional resource.

Biotin Notes

Download PDB Here and view it's details Here.


Streptavidin Notes

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