Hi Darrell, I've often seen Chimera's MMTK energy minimization go nowhere as you observe. I think basically it is taking miniscule steps, essentially zero, because there is a bad clash or extremely long bond. In fact whatever is causing the energy to be astronomical is what is probably what is causing the minimizer not to take any step bigger than 0. I don't know a good way to see where the high energy is coming from. Maybe you could try minimizing some very small set of the atoms with the rest fixed. By trying minimizing different movable sets of atoms you could see where the high energy is coming from. I'm not sure this will work, because it could be that the step size is forced to be tiny even if the high energy is caused by fixed atoms. You'd have to experiment to figure that out. I'll be interested to hear what you figure out. Another idea that could help you figure this out -- the Chimera "minimize" command has a new "fragment true|false" option that allows you to minimize just part of a molecule. It is different from holding atoms fixed. With fixed atoms as you have tried, the fixed atoms still contribute to the force field. With "fragment true" and the minimize command only the specified atoms contribute to the force field, the others being completely ignored. This fragment option is not available in the minimize dialog. It was added in Chimera 1.6. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/minimize.html I see it would be nice to have Chimera be able to color your atoms and bonds in a way that reflects the energy terms for involving each atom and bond. Not sure if that info is available in the dynamics library Chimera uses, MMTK. That would allow you to quickly spot the problem. Tom
Hi there,
I'm trying to minimize a protein after mutating a residue with the Rotamers panel. I first do a Check Clashes and select the clashing atoms. Then I expand the selection using Zone to<5 A. I use these selected atoms as the non-fixed atoms and the unselected atoms as the fixed ones. When I then run the minimization with the appropriate settings, I get an RMSD of 0.000 A for each step, even though the step size is 0.02 A. Nothing moves. Same thing if I have no fixed atoms.
Am I in a local minima? Is that why nothing moves?
The energy is very high (from the Reply Log):
Potential energy: 222274199.525130, Gradient norm: 833984762.552943 Updated 6029 atoms. RMSD: 0.000000 Finished 1 of 5 steepest descent minimization steps
Any ideas? I do have some hetero atoms...
Thanks, Darrell