[Chimera-users] Docking with UCSF Chimera

Elaine Meng meng at cgl.ucsf.edu
Wed Sep 25 08:32:06 PDT 2019

Dear Su,
Your ligand file is a 2D SDF, not a 3D structure of a molecule.  You have to use a 3D structure, not this flat drawing, which also has bonds much too short for a real molecule.  The chemical recognition in Dock Prep requires reasonable bond lengths and a 3D structure (which might be flat if it were benzene, but sucrose should not be flat).

Furthermore, sucrose is a disaccharide and this SDF is clearly a monosaccharide (only one sugar ring).

One way to get a 3D structure is to fetch into Chimera using a Pubchem CID.  E.g. go to the PubChem Compound database and search for what you want, then use Chimera menu: File… Fetch by ID, choose PubChem, and enter the CID for that compound.

If sucrose is what you actually want, it is Pubchem CID 5988:

Below I attached a picture from opening your SDF and also using Chimera command: open pubchem:5988
Your SDF is on the left, the Pubchem structure on the right.

Also to note is that Autodock Vina docking is not “inside” Chimera.  This tool in Chimera connects to an outside web service that is running Autodock Vina, which is developed by another group.  You should be aware that the web service does not allow very much sampling, so if you want to a very in-depth search you would need to use a different approach.  This is explained in the help page:

Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Sep 25, 2019, at 12:26 AM, Su Datt Lam <sudatt.lam at gmail.com> wrote:
> Dear Chimera,
> I am trying to use your software to run molecular docking of sucrose onto a structure. I've provided the ligand and also the receptor structure in the email. 
> I've added the charge for the ligand (using Tools->Structure editing-> Add charge) and selected Gasteiger ad the charge method. After that, I prep the ligand (using Tools -> Structure editing-> Dock Prep). Then, I performed the docking thru Tools ->Surface/Binding Analysis ->AutoDock Vina.
> Vina program managed to run, but with some errors. The ligand bound to the structure is not the right structure of sucrose, but a hairball.  I suspect there's something wrong with the Ligand prepping method in chimera that causes the structure to go crazy. Can you help me with this problem? 
> Many thanks,
> Su
> <Fructose.sdf><full_model_8117_1.pdb>_
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