[Chimera-users] Saving relaxed system in pdbqt format for Vina

[Elaine Meng]

Dear Jatin,
Chimera itself does not write pdbqt format.  I recommend you save the structure from Chimera in PDB format

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb>

... and then (not using Chimera any more) obtain and use the prepare_receptor4.py script from Autodock Tools as described in this page:

<http://autodock.scripps.edu/faqs-help/how-to/how-to-prepare-a-receptor-file-for-autodock4>

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


> On Sep 9, 2020, at 3:55 PM, Jatin Kashyap <jk435 at njit.edu> wrote:
> 
> Dear Chimera Community Members,
> 
> I am new to this code, and tried to navigate through this wonderful piece of code by myself. 
> However, I am not able to find a way to save the relaxed system(relaxation performed in UCSF Chimera) in pdbqt format.
> 
> Can anybody please help me to understand how I can do it, OR am I doing something completely wrong?
> 
> Thank you for your time, and efforts.