Syed Zayyan

afaik isn't pybel an openbabel wrapper for Python, I might be wrong. And also I think there is a UI tool for openbabel for mac https://macinchem.org/ibabel/

so only half of the molecules are acting this way and they do happen to come from another receptor but I don't see how that could have caused problems

I downloaded smina through conda and the only version of openbabel on conda list is : openbabel 3.1.1 py310h4b1c3e3_4 conda-forge

I don't think so............as in processing the .sdf files or initially when converting to PDBQT files

This is an example of the many. I am actually docking it to 6D9H, which is also attached. The SMILES: Cc1ccc(-c2nc(N)nc(N3CCN(C)CC3)n2)cc1

This is an example of the many. I am actually docking. I am actually docking it to 6D9H, which would is also attached. The SMILES: Cc1ccc(-c2nc(N)nc(N3CCN(C)CC3)n2)cc1

This is an example of the many.

hello! I tried docking some compounds using SMINA. Scoring and SDF Files are generated however when reading them back into Python with RDkit I encounter this weird issue: 09:44:49] Explicit valence for atom # 9 N, 4, is greater than permitted [09:44:49] ERROR: Could not sanitize molecule ending on line 55 [09:44:49] ERROR: Explicit valence for atom # 9 N, 4, is greater than permitted However I can visualise the files using Chimera quite okay. which is utterly confusing!