Assignment III
Otcomes:
- Develop introductory familiarity with minimization routines
of Xplor-NIH.
Objectives:
- Reduce the total energy of the two structures created from
Assignment II.
- Reduce the total energy of 10 structures with varrying sizes
obtained from the PDB.
Details:
Start with the two structures from previous assignment. Perform the
following
operations on the two structures and submit a report of the following
information:
- Energy minimize each of the structures with stadard force field
terms and force constants.
- Create a plot of the total energy term as a function of
iterations
(number of iterations should be at least 10,000).
- Quantify and observe the bb rmsd between the starting and
minimized structures.
- Provide a brief discussion of the observed differences (what are
the differences between the two structures and why did it happen)
Record and report the following paramters for the 10 PDB structures:
- Record the change in the final energy between the initial and
final states
- Record the observed bb_rmsd between the two states
- Create a plot of the delta_E versus bb_rmsd for the 10 structure
- Include a trendline in this graph (include the equation for the
trendline and R^2 measure).
Submit:
Submit a short report illustrating and summarizing the above
information. In addition to the report submit the four pdb files of
your helix/sheet.
Other Notes:
In your minimizations play around with various components and note any
change
in the final Etotal. It is likely that you could achive a better result
by
altering some parameters. Note any abnormalities of your final
structure and
see if you can alter the force field to focus on specific problems.
Make
sure that you get E_Total at 0-th and final iteration individually.
Required Material: