Vina 1.2.5 Results Not Fully Displayed in PyMOL_3.0

[Kephas24]

Dear Dr. St. Mart,
My name is Kephas, I have been utilizing AutoDock Vina for my studies and have encountered an issue that I hope you can shed some light on, given your expertise in PyMOL and computational structural biology.
I am specifically comparing results obtained from AutoDock Vina versions 1.1.2 and 1.2.5. When visualizing the docking results from Vina 1.1.2 in PyMOL, I am able to successfully view all twenty predicted poses/modes. However, when attempting to visualize results from Vina 1.2.5 using the same procedure, I encounter a problem where PyMOL does not display all the resulting poses.
I have ensured that the output files from both versions are generated with the same configuration parameters (other than those inherent to the version differences, if any).
I would be incredibly grateful if you could offer any insights or suggestions on how to resolve this issue.

Sincerely,
Kephas

[Kephas24]

[Kephas24]

There are some NA in the reults! If I remove them, the results become normal; where does the problem lie, and how can I solve it?

[rwxayheee]

Hi @Kephas24

I've tried reproducing the problem on Windows, but I haven't been able to replicate it on my end. If it's possible, would you be able to share the input and output files? This would greatly help us with tracking the issue.

My guess for a possible source of NUL is the input ligand PDBQT. If you do observe these in the input ligand PDBQT, then it could be a ligand file writing issue, and we would like to know what package and which version you prepared the ligand file with. But if you have used the exact same input files for v1.2.5 and v1.1.2, then that is not a valid guess. When encountering lines with NUL in the input, vina v1.2.5 keeps and returns them to the output (and could potentially write files in a mix encoding, or a mixed line ending convention?), but v1.1.2 would consider it as Unknown or inappropriate tag and reject the input.

Overall it seems like the invalid characters are relatively isolated, and don’t impact the structure of the rest of the file. A quick workaround would be to strip the NUL characters.