[Chimera-users] Amber Force Field

Forbes J. Burkowski fjburkow at plg.uwaterloo.ca
Fri Apr 13 07:09:11 PDT 2012


I have noticed that scripts can start with:

import MMTK
import MMTK.ForceFields
from MMTK.ForceFields import Amber94ForceField

We are doing some side chain packing studies that would benefit from the
availablity of "easy" force field calculations.  Currently, the algorithm
works with useRotamers() to set two neighbouring rotamers and this is
followed by a simple energy calculation to evaluate the interaction energy
between the two rotamers.  Right now, the energy calculation is only a bit
more sophisticated than a steric collision detector.

Question:  Can we use some functions in the MMTK.ForceFields module to get
an improved energy calculation?

Any suggestions would be appreciated.


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