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

[Elaine Meng]

In the correction I sent, you never have to save as PDB yourself, just run the tool directly in Chimera on the currently open structure after designating that model as the receptor and another currently open model as the ligand.  However, I believe that will still use an intermediate PDB file as the input to the autodock receptor prep script.  It does not use any charges the structure may already have in Chimera.

In summary, there is no way to save any pre-existing atomic charges in Chimera into a pdbqt file.

However, if I recall correctly, AutoDock Vina does not use the charges in the pdbqt file anyway; only the original AutoDock program used them.  AutoDock Vina scoring does not use charges at all.  You can read about this in the Autodock Vina publication, reference and link given in its homepage:
<http://vina.scripps.edu/>

Elaine

> On Sep 9, 2020, at 5:33 PM, Jatin Kashyap <jk435 at njit.edu> wrote:
> 
> Okay, I think I got it. However, I have one general question about first method: if I first save the minimized structure as PDB and then use the script to covert it into pdbqt. Doesn't the charges shall be lost in the process? As per my brief knowledge about these two formats is, PDB doesn’t saves the charges and atom types but PDBQT does. So if we convert the former into later, how does resultant PDBQT files gets the charges data when its parent file(.PDB) doesn’t have it stored at the first place. 
> 
> ——
> Jatin Kashyap 
> 
> 
>> On Sep 9, 2020, at 7:28 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> 
>> Correction, you can actually run the Chimera "Autodock Vina" tool (in menu under Tools... Surface/Binding Analysis) and it will use that autodock prep script automatically and generate a pdbqt file.
>> 
>> The reason I didn't mention that before is that the docking step of that tool no longer runs unless you install Vina locally, and I also don't recommend using that tool for docking in general since even if you install Vina locally, it does not allow an adequate amount of sampling. Instead, for better sampling, you should run Vina directly (not using the Chimera tool).
>> 
>> However, experiments reveal that even though the docking step of the Chimera tool fails (because I did not install Vina locally), the prepping steps are still carried out.  You may need to specify a ligand model in addition to the receptor in order for it to work.  Even if you don't have one that you care about for this  receptor, you can just open some random small molecule and specify that, and then just throw away thae ligand output file. All you need to do is to enter a location and filename in the "output" section of the Chimera tool and you will get filename.receptor.pdbqt and filename.ligand.pdbqt in that location, assuming that your input structures do not cause problems for these scripts.
>> 
>> The tool includes some options for prepping the receptor and ligand, as described in the manual page.
>> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>
>> 
>> Ignore the stuff about downloading Vina, you don't need to do that if you're just trying to write pdbqt.
>> 
>> 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 4:10 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>>> 
>>> 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.
>>> 
>>> 
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>> 
> 
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