-
Notifications
You must be signed in to change notification settings - Fork 0
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
energy_file = "checklines.txt" #1
Comments
Hey! I appreciate you investigating the matter. Essentially, it's a text document containing all compound names along with their binding affinities. It ought to be named 'Energy.txt' since the 'binding_energy.py' script saves the energies in that file. Thanks for catching the error. I've made the necessary updates to the 'full_dir.py' file. |
After I changed it to Energy.txt, the extracted "full_dir" directory was empty. |
The purpose of the full_dir.py script is to duplicate the dlg files of the ligands into a new directory. This allows you to extract coordinates from these files to obtain a protein-ligand complex. In the full_dir.py file, there's a variable named 'dir', initially set as 'dir = lines[6:13]'. It should be adjusted to 'dir = lines[:13]'. Alternatively, you can directly download the updated file from the repository. |
OK! Thank you very much. I have a question for you. When I was sorting out the ad_gpu docking results, I found that the small molecule was protonated, resulting in an abnormally low affinity (-30kcal/mol). This result bothers me very much, and I don’t know whether to keep it. |
You can check the protonation state using different software, just set the pH to 7.4. If the protonation makes sense biologically, then keep the molecule. Also, try docking with the uncharged version to see if the charge is affecting the result. |
What file is this "checklines.txt"? How did you get it?
The text was updated successfully, but these errors were encountered: