sarisabban / notes Goto Github PK

Hello,
I really enjoyed the amazing explanation on the use of AutoDock vina :)

Since, I have begun incorporating this guide into my own project. I had a question regarding the receptor function & the generated output 'receptor.pdbqt'. I followed the following steps:

1. grep ATOM protein.pdb > R.pdb
2. python AutoDock.py -r R.pdb

In step 1, there are no water molecules that are generated inside R.pdb.
However, when I run step 2, the generated receptor.pdbq has the following lines:
ATOM 1 O HOH 1 93.344 30.073 43.622 0.00 0.00 +0.000 OA

Is this to be expected?
Any advice would be greatly appreciated :)
Regards,
Akshat

Dear Expert,

I am following your instructions to run autodock.py. However, I met the message as below:

python3 /home/leo/Desktop/autodock.py -r /home/leo/Desktop/R.pdb

Traceback (most recent call last):
File "/home/leo/Desktop/autodock.py", line 65, in
import pymol
ModuleNotFoundError: No module named 'pymol'

What should I do solve the problem? I installed pymol with sudo apt install pymol

When you have time, could you help me?

Thank you very much for your help,

Kind regards,
Le Phuong.