Ligand protein interaction can't run

[Fahryshitpost]

Hi dear, I ran into problem that I can't run the code on "parameter to generate the topology" part because the ligand_gaff.pdb couldn't be produced, how to fix this issue? thank u in advanced and have a blessed day

[pablo-arantes]

Hi @Fahryshitpost,

Sorry for my delay. As far I understood from your screenshot, you have two ligands in the same file. It will not work with two ligands. The notebook is for one ligand and protein. You need to modify the code to make it works for two ligands.

I hope it helps.

Thank you.

[pablo-arantes]

BTW If you want to run with two ligands simultaneously, you can check the following notebook: https://colab.research.google.com/github/pablo-arantes/making-it-rain/blob/main/Protein_2ligands.ipynb

Thank you.