[Chimera-users] Amber Force Field
conrad at cgl.ucsf.edu
Fri Apr 13 10:38:32 PDT 2012
Chimera's "Structure Editing -> Minimize Structure" tool (or the
"minimize" command) may be used to do this. The tool reports the
initial energy of the system in the Reply Log. If you give zero as the
number of steps for both steepest descent and conjugate gradient
minimization, then Chimera should return immediately.
On 4/13/12 7:09 AM, Forbes J. Burkowski wrote:
> 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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> Chimera-users at cgl.ucsf.edu
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