[Chimera-users] Batch energy minimisation

Eric Pettersen pett at cgl.ucsf.edu
Fri Aug 24 11:37:13 PDT 2012

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:


> 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 Pettersen
                        UCSF Computer Graphics Lab

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