[Chimera-users] Minimize with fixed atoms

Eric Pettersen pett at cgl.ucsf.edu
Mon Apr 2 18:56:36 PDT 2012

Another thing you could try is to change the Detect Clashes criteria  
to show only the very worst clashes and try to partially relieve those  
"by hand" by changing torsion angles of relevant bonds.


On Apr 2, 2012, at 6:49 PM, Tom Goddard wrote:

> 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
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

More information about the Chimera-users mailing list