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).
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.
Combine Production Trajectories while Stripping the Water Molecules
trajin ../003.SANDER/10md.trj 1 1000 1
- trajin tells ptraj to "read-in" the file which comes after it
- ../003.SANDER/10md.traj is the file to be "read-in"
- 1 1000 1 tells ptraj to use the first to the 1000th snapshot of the trajectory. The third number, "1", is telling ptraj to read-in every frame. If this last number were "2", then ptraj would read-in every-other snapshot, "10" would be every 10th snapshot and so on..
trajin ../003.SANDER/11md.trj 1 1000 1
- This will do the exact same as the first trajin cmd (command), except now we're analyzing a different trajectory - 11md.traj.
trajout 1df8.trj.strip nobox
- trajout tells ptraj to write a new trajectory file, combining the two above trajectories.
- 1df8.trj.strip is the name of the new trajectory to be made by trajout
- nobox is essentially a house-keeping cmd, where the periodic box information (The optional keyword "nobox" will prevent box coordinates from being dumped to trajectory files; this is useful if one is stripping the solvent from a trajectory file and you don't want that pesky box information cluttering up the trajectory and messing with other programs)
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).