[Chimera-users] Amber Force Field

Elaine Meng meng at cgl.ucsf.edu
Fri Apr 13 10:57:37 PDT 2012

Hi Forbes,
The minimization tool reports the total energy, not any breakdown into components (electrostatic, VDW, strain) or interactions between sets of atoms.  However, the "minimize" command has a "fragment" option for ignoring all but the specified residues, so you could at least limit what is considered the total system. That also makes the calculation faster, although single-point energy calculation (0 steps minimization) should already be pretty fast.

Example (and see also "nogui true"):

minimize spec :13.a,17.a fragment true cgsteps 0 nsteps 0


On Apr 13, 2012, at 10:38 AM, Conrad Huang wrote:

> 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.
> Conrad
> On 4/13/12 7:09 AM, Forbes J. Burkowski wrote:
>> Hi:
>> 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.
>> Cheers,
>> Forbes
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