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 MD (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.
ptraj - Analyzing Your Data
ptraj is an analysis program included in the AMBER suite (AMBERtools) designed in part by Dr. Thomas Cheatham. See this website.
A useful and recommended program to write is:
#!/bin/csh ptraj parameter_aka_topology_filename.parm ptraj_input_filename.1.in > ouput_results_ptraj.1.out exit
#!/bin/csh will be in nearly all of the programs you will write - unless you dabble in Cpp or G77. It tells the shell to treat the contents of this here file as if the contents were being typed in the shell by hand.
ptraj has been aliased in your .cshrc file and will initialize ptraj once read by the machine.
parameter_aka_topology_filename.parm is the .parm file you would like to specify.
ptraj_input_filename.1.in is the set of instruction you want ptraj to read and perform, in an input file (This would be "ptraj.concatenate.strip.trj" in the coming examples).
exit will exit from ptraj when the ptraj_input_filename.1.in has completed its instruction(s).
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.trj 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.trj.
trajout 1df8.trj.strip nobox
- trajout tells ptraj to write a new trajectory file, combining the two trajectories - 10md.trj and 11md.trj - from trajin.
- 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)
- So you're left with a file "ptraj.concatenate.strip.trj" with the following in it:
trajin ../003.SANDER/10md.trj 1 1000 1 trajin ../003.SANDER/11md.trj 1 1000 1 trajout 1df8.trj.strip nobox
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).
trajin 1df8.trj.strip 1 2000 1 trajout 1df8.com.trj.stripfit reference 1df8.com.gas.leap.crd
- reference tells ptraj that you want to specify a reference file - snapshot - for which to compare your trajectory (file with many snapshots) to.
- 1df8.com.gas.leap.crd is the reference file. This file is very important and you ought to be thoughtful about your selection of this file. Usually, when possible, one wants to use the experimental structure as the reference. Referencing the experimental structure 'usually' provides the most informative results. But, if done thoughtfully, a non-experimental reference could be informative, too...
rms reference out 1df8.rmsd.CA.txt :1-118@CA
- rms tells ptraj you want to perform an rms analysis
- reference tells traj to use the reference file, specified in the previous line
- out tells ptraj to create a temporary file out for which to store calculations during the analysis
- 1df8.rmsd.CA.txt is the name of the file with the RMSD analysis results. This is the file you will use with your plotting program..
- :1-118@CA tells ptraj you would like to analyze the RMSD of the alpha-carbon atoms CA residues 1-118. The syntax is silly, but such is life.