Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Running without receptor #256

Open
ale94mleon opened this issue Dec 5, 2023 · 2 comments
Open

Running without receptor #256

ale94mleon opened this issue Dec 5, 2023 · 2 comments
Assignees

Comments

@ale94mleon
Copy link

Hi, I am executing the following command:

vina_1.2.5_mac_x86_64 --receptor this_dir_is_empty --center_x 1.2 --center_y -5.5 --center_z -5.1 --size_x 23.7 --size_y 15.1 --size_z 25.2 --ligand ligand.pdbqt --out ligand_out.pdbqt

And it runs, although this_dir_is_emtpty is an empty dir. The same happens if I just use an empty *.pdbqt file as receptor.

I got even the poses info:

mode |   affinity | dist from best mode
     | (kcal/mol) | rmsd l.b.| rmsd u.b.
-----+------------+----------+----------
   1            0          0          0
   2    0.0001106      12.56       13.9
   3    0.0001106      14.74      16.04
   4    0.0002842      14.17      15.34
   5      0.00478      7.914      9.297
   6      0.01306      5.024      6.531
   7      0.01432      11.85      13.03
   8      0.02745      5.841      7.064
   9      0.03524      6.131      7.618

I was expecting an error.

@diogomart
Copy link
Member

I also thought it would raise an error, but there's nothing wrong about docking into nothing.

@rwxayheee rwxayheee added this to the Maintenance Release milestone Jan 11, 2025
@rwxayheee
Copy link
Collaborator

Added to Maintenance Release (if we want a warning, or purposefully empty receptor or empty ligand). I agree that in some scenarios, it can be useful not to raise an error.

@rwxayheee rwxayheee self-assigned this Feb 18, 2025
rwxayheee added a commit to rwxayheee/AutoDock-Vina that referenced this issue Feb 18, 2025
add a warning when when calling parse_receptor_pdbqt returns an empty receptor (ccsb-scripps#256)
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

3 participants