[Chimera-users] Minimize with fixed atoms
goddard at sonic.net
Mon Apr 2 18:49:59 PDT 2012
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.
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
> 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...
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