[Chimera-users] Query regarding chimera tool

Elaine Meng meng at cgl.ucsf.edu
Tue May 9 08:04:41 PDT 2017

On May 8, 2017, at 10:54 PM, bushra TAJ <bushraistaj at gmail.com> wrote:

> Hello Sir
> I want to do some docking studies of my own synthesized compounds. I found them very active in some anti-cancer assays.
> I will use AUTODOCK for this purpose. I have got the Pdb file of my target protein from PDB database. 
> My problem is how to make pdb of my molecule (input file for autodock) can I use chimera for that??
> I have chem-draw file format of my molecules will that open in chimera to make their pdb format.
> Regards

In the menu under Tools….. Surface/Binding Analysis:

There is a “Dock Prep” tool for preparing PDB files.  There is also an “Autodock Vina” tool that will make prepared files in pdbqt format, but it will also run Autodock Vina docking (in other words, the prepared pdbqt files are a by-product but you could also use them as input to something else).

You should look at the manual pages for more information.


Also in the future please send Chimera questions to chimera-users at cgl.ucsf.edu and include a useful subject line like “preparing molecules for docking.”  Messages to my individual email address may not get answered.

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

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