[Chimera-users] Minimize with fixed atoms
Hurt, Darrell (NIH/NIAID) [E]
darrellh at niaid.nih.gov
Mon Apr 2 18:30:46 PDT 2012
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...
Darrell Hurt, Ph.D.
Section Head, Computational Biology
Bioinformatics and Computational Biosciences Branch (BCBB)
31 Center Drive, Room 3B62B, MSC 2135
Bethesda, MD 20892-2135
http://bioinformatics.niaid.nih.gov (Within NIH)
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