Channels in training script are different from those in your Supporting Information table s1 about deeppocket HOT 6 CLOSED

Yes, gninamap file is used to create the gninatype files which specify the atom type a particular atom is. When these files are loaded into libmolgrid, libmolgrid assigns these atoms to different channels based on whether it is a "receptor" or a "ligand" atom and based on the atom type identity. The first 14 channels represent the receptor atoms - theres probably a better way to do this but its a hack that worked at the time. So the first 14 channels represent the atom types that are given in our supporting information.

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Thank you for your quick response. So, you mean libmorgrid considers Bromine Iodine Chlorine Fluorine (which are 4 diferent channels in gninamap file) as channel 5 (number from 1), Nitrogen NitrogenXSAcceptor as channel 6 (which are 2 diferent channels in gninamap file) etc.. Is this right? So, what do the other 14 channels represent, and where can I find the definition of the whole 28 channes in libmolgrid files?

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you can see the ligand atom types here: https://github.com/gnina/libmolgrid/blob/master/include/libmolgrid/atom_typer.h - the atom types are at the bottom of the file

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So, does it mean that if I use the defaultGninaReceptorTyper, I wiil get the same representation of protein as in your paper?

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Yes you should when you load a grid with it, however you have to be careful not to save gninatypes files using that typer

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Thank you very much for your patience. My doubts have been resolved. I will close this issue.

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