Hello,
I don't know which "Save" button you are talking about, but I don't think any of them changed.

However, if you are using the Autodock Vina dialog, the files will be saved automatically according to the location that you specified as "Output file" in the dialog.  For example if I use the dialog as shown in the attached image, I would automatically get files in directory ~/Desktop/ named

adtest or adtest.pdbqt -- docking results
adtest.receptor.pdbqt -- prepared receptor 
[etc.]

... as explained in the help page:
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>

So just put in the "Output file" area the location and name that you want to use. If you already ran AutoDock Vina, just show this dialog again to check where you already put them.

Although you can use menu: File... Save PDB, it does not save pdbqt format, only pdb.  For the pdbqt format files, you just have to find where they were written when you ran AutoDock Vina.

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




On Dec 6, 2022, at 8:23 PM, Kumar Pratyush via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

Hello Sir/Mam,
I am not able to save complex of docked output.pdbqt and protein.pdbqt as save button is not getting active.
I used to do the same protocol earlier with ease but now not able to execute.
I tried by uninstalling and re-installing but still things are not working smoothly. Please help.

Thanks & Regards