[Chimera-users] Get Minimization Energy

Leonard Zhao l84zhao at uwaterloo.ca
Fri Nov 26 09:15:33 PST 2021

Hi Elaine,

I will only be using the energy value to compare with other minimizations done on the same structure, and MM/MD methods have too high of a computational cost since I will be performing thousands of minimizations on the same structure. I am hoping that, even though the energy values are only local minimums, they can still be used for comparison with repeated minimizations on the same structure with a slight perturbation each time.

Leonard Zhao
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Friday, November 26, 2021 11:58 AM
To: Leonard Zhao <l84zhao at uwaterloo.ca>
Cc: chimera-users at cgl.ucsf.edu <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] Get Minimization Energy

Hi Leonard,
The values are not really meaningful except relative to one another for the same structure (e.g. minimization reduces the value), and not for comparing between different structures.  So while this does not answer your technical question per se, I don't think you can get much information by saving these values.  Some other dedicated MM/MD programs may give a more useful/valuable breakdown of terms, but this single, usually huge number doesn't tell you much of anything.

Furthermore, minimization just gives you a local minimum, not generally the global mininum, and it's not the free energy of the system either way.  So for example if a mutated structure has a higher number than the wild type after minimization, you still don't know whether it is more or less stable than the wild type protein.

Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Nov 26, 2021, at 8:40 AM, Leonard Zhao via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> Hello,
> I am running a Python script to perform multiple structure minimizations and I need to extract to final potential energy from each minimization. I see that the potential energy is usually reported in the Reply Log, but when IDLE is open, it is instead redirected to IDLE. Is there any way to redirect it back to the Reply Log so I can more easily extract it in my script, or is there some other method to easily extract the energy value programmatically?
> Thanks,
> Leonard Zhao

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