Ranjee

Hi, I want to ask you about how to getting the center xyz of many ligands automatically in python script, when computing map. @rwxayheee

Sorry, I was using vina python API, not ad4, to try automatically set the center as ligand's center. ``` v.set_receptor(rec_file) vina_box_size=[37,37,37] v.set_ligand_from_file(lig_file) v.compute_vina_maps(center=center, box_size=vina_box_size) ```

I also have questions when dealing with a pdb protein file(pdbid: 5nee) into pdbqt using ADFR. `$ /ADFRsuite-1.0/ADFRsuite_x86_64Linux_1.0/bin/prepare_receptor -r 5nee_pocket.pdb -A hydrogens -o 5nee_pocket.pdbqt Traceback (most recent call last): File...

@diogomart Dear developer, I met the same questions. When there is metal ions such as Mg, the ADFR can't convert it into pdbqt file. So it is impossible to use...

I have an important question to ask you: How did you process the numerous pdb files which have ions such as Zn in the dataset in to pdbqt? I find...

I also do not know how to train models on CASF-2016 refined-set and get its pkl model file(for further re-training). The only thing I know is that there is a...

I don't believe the RF-Score could be so awful, is there any potential bug about my code? Is this binary rf-score-vs unable to score any more?

For the second question, you can find in the passage: ``` When evaluating a test set without counterexamples, models trained with counterexamples perform worse than their counterparts trained without them...

Hi, just ask you to make sure the built-in `crossdock_default2018.caffemodel` is trained on `crossdock2020 dataset` or `PDBbind_v2019_refined-set`? I only know its redocking power is tested on PDBbind_v2019_refined-set, and `crossdock2020` is...

Hi professor, I noticed all "Gnina 1.0" related papers are published before 2018, so the caffemodel of default2018 like redock_default2018 are surely trained after that. However, I could not find...