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

Eric Pettersen pett at cgl.ucsf.edu
Tue Nov 17 10:56:29 PST 2015

Hi Albert,
	The fact that your file is 2D is problematic for Chimera in determining atom types and therefore correctly protonating your molecule.  If you can figure out the SMILES equivalent for your structure you can use Chimera’s Build Structure tool to convert the SMILES into its 3D equivalent.  Otherwise there are various places on the web to convert a 2D SDF to 3D.  Here’s one:  http://crdd.osdd.net:8081/webcdk/2D-3D.jsp <http://crdd.osdd.net:8081/webcdk/2D-3D.jsp>
	Once you have a 3D version of your structure, everything Elaine said applies.


	Eric Pettersen
	UCSF Computer Graphics Lab

> On Nov 17, 2015, at 9:05 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 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"
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/dockprep.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addh.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addcharge.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/write.html>
> (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.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vina.html>
> So, you probably meant #1 above but I included #2 just in case. I hope this helps,
> 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 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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