Parameters for Molecular Mechanics
General Principles and Issues Remember: Goal is parameters that “fit in” to the force field. Therefore: We must understand where the built-in parameters of that particular force field came from.
General Principles & Issues...
Some Recipes
Parameters based on other parameters
Extrapolating based on bond-lengths comes from correlation between Lengths and Force constants:
AMBER Parmeters taken from MM3
However, the resulting parameters correlate well with existing ones.
Parameters based on experimental data
Transfer force parameters from analysis of vibrational spectra
Fit non-bonded parameters to simulate pure fluid properties
OPLS non-bonded potential between atoms i and j:
Comparison of non-bonded parameters*:
Extract equilibrium parameters from known structures.
HOWEVER...
Fit parameters to give experimental geometries
Parameters from theoretical calculations
Direct evaluation... High level ab initio bond lengths vs experimental
Direct evaluation... Force constants for bond stretch:
Matching Calculated Data sets... II. Step-Wise Approach (Hopfinger & Pearlstein, 1984):
Step wise...
Matching Calculated Data sets... III. Global Approach (Cannon, 1993).
Hybrid parameters sets… Consider the AMBER force field. Parameters come from...
Hybrid parameters sets…
Issues for Metals and Metalloproteins
Appropriate Experimental data is limited
Three general MM approaches… (see Hay, 1993)
Three general MM approaches… Pros and Cons:
Are charges needed?
Example: Rubredoxin-like Center
What’s been done?
Email: wampler@bmb.uga.edu
Home Page: http://bmbiris.bmb.uga.edu/wampler/ibsw00
Other information: References