-
Notifications
You must be signed in to change notification settings - Fork 24
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
How to test the vina_dock.py program #18
Comments
Dear Navya, |
Hi, I am trying to run the command : python vina_dock.py -i smiles.smi --no_protonation -o/ --output output.txt |
Hi, please run command: python vina_dock.py -i smiles.smi --no_protonation -o output.db |
Hi GuzelMinibaeva, Thank you for your response. Am I missing a pdbqt file ? Please help me with this. Thank you, |
Hi Navya, for the first run you should use -p with a path for your pdbqt file and -s with a path for your setup file with grid box coordinates, these command line arguments are necessary for docking. Example: Protein and setup files can be prepared in a standard way. Example of a file with grid box coordinates:
Kind regards, |
Hi @GuzelMinibaeva, I am getting the same error. It seems that database isn't being created at first run.
The command I am trying to execute:
If I solve this issue then I promise that i will send PR. |
Hi, @AnzorGozalishvili, could you attach your input files to reproduce this behavior? It seems like a simple issue. |
It worked locally on my laptop. I amn't able to run it in Google Colab. This is the issue, probably. |
Hi @DrrDom There was some issue related to creating DB. I run this in advance to manually create db.
protonation is set to False since I didn't have an license for Here is the command I was running
|
I am trying to run : python vina_dock.py -i smiles.smi --no_protonation -o/ --output output.txt
Traceback (most recent call last):
File "/home/ubuntu/Desktop/rdkit-scripts/vina_dock.py", line 473, in
main()
File "/home/ubuntu/Desktop/rdkit-scripts/vina_dock.py", line 453, in main
add_protonation(args.output)
File "/home/ubuntu/Desktop/rdkit-scripts/vina_dock.py", line 54, in add_protonation
protonate, done = list(cur.execute('SELECT protonation, protonation_done FROM setup'))[0]
sqlite3.OperationalError: no such table: setup
Could you please help me resolve it or do I have to give more information while running it ?
Thanks in advance,
Navya
The text was updated successfully, but these errors were encountered: