2010 AMBER Tutorial with Biotin and Streptavidin

What is AMBER?

Amber - Assisted Model Building with Energy Refinement - is a suite of about 50 programs that can be used to simulate, study 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.

Analyzing Your Data Using 'ptraj'

ptraj is an analysis program included in the AMBER suite (AMBERtools) designed in part by Dr. Thomas Cheatham.

Sample Skripts

RMSD

RMSD - root mean-square deviation - can be used to measure the distance an object moves relative to another object. For example, one could use an RMSD analysis to measure the movement of the backbone atoms of a group of residues within a protein, using the experimental structure as the reference structure (ptraj will measure the RMSD between each object specified in the ptraj script - see below - to the experimental structure).

Biotin Notes

Download PDB Here and view it's details Here.