[Chimera-users] Fwd: chimera minimize option

Elaine Meng meng at cgl.ucsf.edu
Mon Oct 17 13:59:21 PDT 2016


Hi Jacqueline,
I haven’t seen this, at least when the sidechains have room to relax freely.  Maybe in your case, they are smashed up against some other atoms in such a way that prevents relaxation to the preferred planar state.  Minimization will only find a nearby local minimum, not cross energy barriers to find a lower minimum.  Although there is no reasonable way for users to edit the force field, I don’t expect this to be a problem of the force field (which is well established).

Things you could try include:

(1) run more steps of minimization

(2) try to resolve the steric conflict somehow, which could be by manually rotating bonds or even running some molecular dynamics.  However, keep in mind that such interventions could make your structure worse and/or less realistic.  See “Adjust Torsions” in the Build Structure tool, and the “Molecular Dynamics Simulation” tool (in Chimera 1.11 and newer).
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/md/md.html>

For minimization, you can specify as many atoms as “fixed” (frozen) as you want, and whether they are the selected atoms or the unselected atoms.  If you wanted all atoms to move, don’t bother selecting, just set “fixed atoms: none”.  Still, if you are only minimizing, things generally won’t move that much.
I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Oct 17, 2016, at 1:00 PM, Jacqueline Vitali <jackie.vitali at gmail.com> wrote:
> 
> It puckers ASN and ASP (and probably other amino acids).  (I run it to relieve steric conflicts only)
> 
> How do you fix this?
> 
> And can you run it with the whole protein selected?
> 



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