[Chimera-users] Minimize

Alex Gawronski alex.gawronski at gmail.com
Tue Aug 4 10:21:25 PDT 2009

Thanks for the info!

I was just worried that the added hydrogen atoms would not be in the minimal
position. They do move a little from the minimization. Do you think that is

Alex Gawronski

On Tue, Aug 4, 2009 at 11:38 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Alex,
> I would never recommend minimization as part of a pipeline to prepare
> structures for DelPhi calculations.  Is there some reason you expect these
> structures to be particularly bad?  The minimization is intended for when
> you have done some manual building, or mutation, or docking, and want to
> clear up some local bad contacts or highly strained geometries.  It is only
> a local minimization, and will not "refine" the structure if that requires
> crossing any energy barriers.
> I don't know what the issue with "spec" and "freeze" are, but they worked
> fine when I tried them today.  There must be a selection for "freeze" to
> have any effect. "spec" only controls which models are minimized, so if you
> only have one model open at a time there is no reason to use it.
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/minimize.html>
> For preparing structures for DelPhi, you might want to look at the Dock
> Prep tool (under Tools... Structure Editing).  It has several structure
> "regularization" options such as changing selenomethionine to methionine,
> removing solvent, removing alternate locations of atoms, and rebuilding
> missing sidechains (although not backbone), as well as hydrogen addition.
>  However, don't bother with the charge addition since that will be
> irrelevant to the DelPhi calculation --- DelPhi looks up charges from a
> separate parameter file.
> <
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/dockprep.html
> >
> Actually "minimize" calls Dock Prep to fix up the structure beforehand.  I
> say just use Dock Prep directly and don't bother with charge addition and
> don't minimize, unless there is some reason to think the structures are
> particularly warped.
> The main thing to worry about for an accurate DelPhi calculation is getting
> the charges and radii assigned correctly from the DelPhi parameter files.
>  You should check the DelPhi log file.  That is a DelPhi issue, fairly
> separate from Chimera.
> I hope this helps,
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>                     http://www.cgl.ucsf.edu/home/meng/index.html
> On Aug 3, 2009, at 1:32 PM, Alex Gawronski wrote:
>  Hello,
>> I'm preparing proteins for Delphi analysis using Chimera's minimize
>> function (from a script). However this process is very time consuming. Is
>> using minimize necessary to get accurate results from Delphi? If not, what
>> is necessary? I've played around with the "spec" and "freeze" parameters and
>> they either seem to have no affect or throw an error (which I submitted as a
>> bug). What do you suggest I do?
>> Thanks,
>> Alex Gawronski
>> Carleton University
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