[Chimera-users] Minimize with fixed atoms

Tom Goddard goddard at sonic.net
Mon Apr 2 18:49:59 PDT 2012

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.


   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...
> Thanks,
> Darrell

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