Dear Elaine,

thank you very much for your answer to this request. I understand that ChimeraX does not provide a direct interface to an AutoDock Vina web server.

However, the functionalities of the "AutoDock Vina" tool in Chimera (1. saving the receptor and the ligand pdbqt files, 2. defining the search volume, and 3. saving an AutoDock Vina input file) besides launching the docking were also immensely useful for us, especially for teaching purposes.

Would it be possible to provide these 3 functionalities also in ChimeraX, for example within the "Dock Prep" tool? The possibility to save a mol2 file is already provided, would it be possible to provide also the possibility to save pdbqt files for the receptor and the ligand?

Thank you in advance for your help.
Ute


From: ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu> on behalf of Luigi Marongiu via ChimeraX-users <chimerax-users@cgl.ucsf.edu>
Sent: Sunday, March 12, 2023 19:10
To: Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu>
Subject: Re: [chimerax-users] Missing Vina on ChimeraX
 
Thank you
Best regards
Luigi
From: Elaine Meng <meng@cgl.ucsf.edu>
Sent: Sunday, March 12, 2023 18:49
To: Luigi Marongiu <luigi.marongiu@outlook.com>
Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu>
Subject: Re: [chimerax-users] Missing Vina on ChimeraX
 
Hi Luigi,
ChimeraX does not have an Autodock Vina interface (a tool to run Autodock Vina).

Although Chimera has an Autodock Vina interface, the Autodock Vina program is not part of Chimera.  Instead this Chimera tool would send your data out to an Autodock Vina web service run by another group, and then get the results back and display them.  That Autodock Vina web service is no  longer available.  With Chimera, however, you can still use its Autodock Vina interface if you also separately download Autodock Vina and install it on your own computer.  However, even this is not recommended because the Chimera interface only allows a very small amount of sampling.  For most scientific research, you should not use Chimera to run the docking, but just instead use Autodock Vina directly.  This is explained in the Chimera help page for its Autodock Vina tool:
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>

After you get docking results from Autodock Vina, however, then you can view/analyze them using either Chimera (ViewDock tool) or ChimeraX (ViewDockX).
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.html>
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/viewdockx.html>

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

> On Mar 12, 2023, at 1:04 AM, Luigi Marongiu via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Dear sir or madam,
> I am using UCSF ChimeraX version 1.5 (2022-11-24). I have been trying to use AutoDock Vina but there is no such command in my version.
> How do I install it into ChimeraX (as shown in many tutorials, Vina is part of Chimera)?
> Thank you.
>
> Best regards,
>
> Luigi Marongiu
> Ph.D., B.Sc. (Hons.)