SoodabehGhaffari

Hello, Sorry for the late reply and thank you for the email. I also tried the nightly version on the offline cluster, but I received the error message below which...

Hello, Thanks for the response. I believe I did not clearly explain my first question. My ligand is in the binding pocket, but the resultant structure from docking is not...

Thank you for the help. I have two more questions: 1. One of the reasons mentioned in that link is the protonation state of ligands and receptors. I prepared the...

Thank you for the help! Just one more question: If we do not have a pseudo atom in Vina output (.pdbqt), do we still need to use "mk_expoet.py"? I am...

Thank you for the response. I am facing another issue, but I am not sure if it is related to mk_export.py. After I use mk_export.py, I get the sdf file...

Thank you for the answer. I believe I need to ask my question more specifically: My receptor has coenzyme (NADPH) and I am having difficulty to prepare the receptor with...

To add more information about my previous question, I decided to prepare the coenzyme separately (as a ligand) and docked it into the receptor, but I ran into the error...

Thank you for the help! I am attaching the sdf file of the coenzyme named NAP.sdf to this email. If you have any suggestions, please let me know. On Thu,...

Thank you for the help! On Thu, Jun 15, 2023 at 5:48 PM Amy He ***@***.***> wrote: > Hi @SoodabehGhaffari , > > I couldn't find the attachment from the...

I pasted my sdf file below: Could you please see what the problem with the sdf is? I open it with Pymol and I cannot see any issue. NAP PyMOL2.4...