Closed SejeongPark8354 closed 2 years ago
Have you solved the problem yet, I have the same problem as you。😂
@nohandsomewujun I haven't solved this problem yet 😭
Sorry for forgetting about this and thanks for the reminder!
I am not sure why the array is empty in your case. Could you send me (hstark@mit.edu) the pdb file and the molecule file for which this is happening so I can try to reproduce it?
Soo, @nohandsomewujun sent me his files yesterday and I was able to reproduce and solve the problem. If you pull the latest update it should work - thanks for pointing out this issue!
The issues: I assumed that waters (HOH) were in separate chains in pdb files and these chains were removed. In the pdb files of @nohandsomewujun, every backbone chain also contained water residues and all chains were removed.
P.S. @nohandsomewujun, I noticed that your ligand file was missing hydrogens. Make sure to add them before running EquiBind!
@HannesStark Thank you very much for taking the time to solve this problem!
@HannesStark Thank you! I will try this again with the latest update.
First of all, Your research has had a huge impact on drug discovery based on AI. Thank you so much!!!
I got the error like below. My Inputs are protein pdb from https://www.rcsb.org/ and 3d ligand conformer from PubChem.
Is there any problem in my input setting? I would be very grateful if you could give me a solution.
Thank you for your work again. :)