Using autobox in a docking search

[rwxayheee]

Dear all,

I realized from issue #264 that --autobox doesn't set grid size or center in a docking search. But Vina will print the following to standard output whenever it receives --autobox, which I feel a little misleading:

Output will be ligand_out.pdbqt
Scoring function : vina
Rigid receptor: receptor.pdbqt
Ligand: ligand.pdbqt
Grid center: ligand center (autobox)
Grid size : ligand size + 4 A in each dimension (autobox)
Grid space : 0.375

In a docking serach (not score_only or local_only), --size_x --size_y --size_z are required with and without --autobox. --center_x --center_y --center_z are optional, but if unspecified it will be 0,0,0. The true grid size and center are not noted in the standard output, when --autobox is used.

It might be helpful to change the standard output, or reject --autobox if using it in docking search is not intended.

Version of the program:
vina_1.2.5_linux_x86_64

I'm running it on: Linux x86_64 (cpe:/o:redhat:enterprise_linux:7.9:GA:server)

Any comments would be much appreciated. Thank you for your time and the excellent work you've done.

[diogomart]

Yeah we should reject --autobox if used in a docking search. That was the original intent as per the help message:

  --autobox                  set maps dimensions based on input ligand(s) (for 
                             --score_only and --local_only)

Thank you for looking into this.

[rwxayheee]

I would like to add this to Maintenance Release, if it's convenient to make some minor improvement to option handling