it is not a big problem as it is easy to correct using a simple script... the generated poses in sdf are missing an end of file; the last line of a sdf should contain $$$$. Some tools like Datawarrior will not load the structure if you do not have it. If you concatenate the files as-is in a multi-sdf, the structures will not be separated by $$$$, unless you correct for it while concatenating.
The other thing... even if the input files are protonated, the output will be un-protonated sdf. While the pose might be very good, it is difficult to get a reliable score using different rescoring tools without protonation of the molecules. Maybe it is linked to the nature of how the poses are generated so nothing can be done for this... Some scoring tools, like Brutenib/ShaEP do not care about it but it will be nice to be able to do scoring consensus. Anyway, I'll make a small script that will call ChimeraX for protonating the ligand in the context of the binding pocket. It is not a big deal as I will find a way around it. Still, it would be useful to get protonated molecules, if you eventually make a new version of Unimol Docking V2.
Hi,
it is not a big problem as it is easy to correct using a simple script... the generated poses in sdf are missing an end of file; the last line of a sdf should contain $$$$. Some tools like Datawarrior will not load the structure if you do not have it. If you concatenate the files as-is in a multi-sdf, the structures will not be separated by $$$$, unless you correct for it while concatenating.
The other thing... even if the input files are protonated, the output will be un-protonated sdf. While the pose might be very good, it is difficult to get a reliable score using different rescoring tools without protonation of the molecules. Maybe it is linked to the nature of how the poses are generated so nothing can be done for this... Some scoring tools, like Brutenib/ShaEP do not care about it but it will be nice to be able to do scoring consensus. Anyway, I'll make a small script that will call ChimeraX for protonating the ligand in the context of the binding pocket. It is not a big deal as I will find a way around it. Still, it would be useful to get protonated molecules, if you eventually make a new version of Unimol Docking V2.
Best, Christian