[Chimera-users] Running AddCharge from the command line

Elaine Meng meng at cgl.ucsf.edu
Wed Nov 21 09:08:21 PST 2018

Hi Samuel,
I should mention that it is not recommended to use the Vina webservice for any pipeline-type calculations.  It is only set up for low-sampling single-ligand runs because it is a shared free resource.  If you want to do “ligand database search” type calculations, you should get Autodock Vina on your own system.  It is open-source/free from http://vina.scripps.edu/

Then you can run database search docking directly using their software (not involving Chimera).  Maybe you’re already using Autodock Vina locally with the Chimera interface.  However, the Chimera interface doesn’t have the database search options or allow for as much sampling as you’d probably want.

However, yes, you can automate ligand prep in a Chimera script without getting dialogs raised if you use the “minimize” command with “nogui true” as explained near the bottom of this page:

… that would automatically run all of dock prep (including addh and addcharge) before minimizing without raising dialogs.  If you didn’t actually want any minimization, it might work if you specified zero steps in the minimize command, or 1 step with all atoms frozen in place.  I haven’t tried either of those myself, however.
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Nov 21, 2018, at 5:30 AM, Samuel FreemanFox <Samuel.FreemanFox at portonbiopharma.com> wrote:
> Hi,
> I am attempting to automate Vina with a python script and want to use addH and addCharge before running Vina, however I cannot run addcharge without the window opening asking me to specify net charges. I was wondering if you could advise on the correct way of writing this command
> Many thanks,
> Samuel Freeman-Fox

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