[Chimera-users] Batch energy minimisation

[Elaine Meng]

Hi Miro,
There is a "minimize" Chimera command, see
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/minimize.html>

However, minimization only reports the total energy of the system -- there is no breakdown into components, as mentioned in this previous post:
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-April/007435.html>

The APBS tool is only in recent daily builds (Chimera 1.7) and is under development. It hasn't been well tested or documented, and there is no Chimera command to run it.  Also, the calculations are not implemented within Chimera but done by an APBS web service provided by the National Biomedical Computation Resource.

<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/apbs/apbs.html>

It is primarily intended for creating an electrostatic potential map, which could be shown as colors on the molecular surface or as isopotential contour surfaces.  The interface might not provide all the controls needed for more detailed uses such as calculating electrostatic binding energies.

Best,
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 Aug 24, 2012, at 11:37 AM, Eric Pettersen wrote:

> On Aug 24, 2012, at 2:40 AM, Miro Moman wrote:
> 
>> Hello,
>> 
>> Searching through the archives, I have found that performing DockPrep in batch mode is quite straightforward:
>> 
>> http://mailman.docking.org/pipermail/dock-fans/2007-May/001043.html
>> 
>> I have also noticed that, when working from the GUI, energy minimisation involves a previous DockPrep step.
>> 
>> I would like to perform the energy minimisation of several protein-ligand complexes, can this be easily done in batch mode?
> 
> You would just take the Dock Prep example you found and meld it with the example of how to loop through data files and perform commands on them, found here:
> 
> http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html
> 
>> Furthermore, I would also be interested of computing the binding energy both prior and after minimisation (possibly including APBS-computed electrostatic terms...). However, this is of secondary importance as it can be easily achieved with other tools.
> 
> In the most recent daily builds there is a tool for computing an electrostatic potential volumetric data set using an APBS web service, but I'm a little hazy on whether this really helps you and I'm certainly no expert on accessing the tool via an API.  If you feel it would be a big help, just say so and the programmer that worked on that (Conrad Huang) may be able to provide more info.
> 
> --Eric
> 
>                         Eric Pettersen
>                         UCSF Computer Graphics Lab
>                         http://www.cgl.ucsf.edu
> 
> 
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