[Chimera-users] how to prepare ligand by command line?

Elaine Meng meng at cgl.ucsf.edu
Tue Nov 17 09:05:36 PST 2015

Hi Albert,
There are two types of dock preparation in Chimera.  They are separate but overlap in function.

(1)The Dock Prep tool, which  does a lot of different things and is generally useful for preparing structures not only for different kinds of docking but for other calculations.  There is no command that runs the whole Dock Prep tool, but there are commands “addh” and “addcharge” to do the hydrogen addition and charge calculation parts, which might be all that you needed.  Then you could save the results to Mol2 file with “write"


(2) Autodock prep scripts (created by Autodock developers) that can be run from Chimera.  These make PDBQT files which I believe are only for Autodock or Autodock Vina docking. These scripts are automatically run by the Autodock Vina tool in Chimera, and there is also a “vina” command with a “prep” option (available in recent daily builds only) to run only the prep and not the docking part.  However, each use of the command requires specifying the receptor molecule and the ligand molecule, and there can only be one of each.  So if you had several ligands they would have to processed in separate commands and you would also need some protein receptor molecule (could be any protein if you don’t care about it) to also be open.


So, you probably meant #1 above but I included #2 just in case. 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

On Nov 17, 2015, at 1:50 AM, Albert <mailmd2011 at gmail.com> wrote:

> Hello:
> I've got a ligand in 2D .sdf format without any hydrogens. I am just wondering how can we prepare this compound for docking? Is it possible to run it by command from Chimera?
> Thanks a lot
> Albert

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