Zhanglab forum

Hi,
I want to dock a small molecule with a protein for project investigation. On the EDock, I have successfully loaded the PDB file of the protein, and the MOL2 file downloaded from PyMOL. But when I submitted, there was an error saying the ligand MOL2 file lack the line with '@MOLECULE'.
How can I solve this problem?
Thank you very much.

Can you send your ligand MOL2 file? We will help you check it. Thank you

Wenyi Zhang

Hi,
It seems that I cannot attach the file to this forum. It says Invalid file extension: sele CoA.mol2
I downloaded the mol2 file from PyMOL where I opened a PDB format of protein-CoA complex and removed the protein component.

You can compress your file by zip and attach the zip archive.

OK, I have attached the file. Thank you so much!

This is the Coenzyme A molecule. Have you tried my file?
Many thanks,
Jinxian

Hi, Jinxian

When I open the file, I only see one line "# created with PyMOL 2.1.0". There may have been several issues when you saved the MOL2 file with PyMOL. I downloaded a COA ligand from the PDB bank. You can check it out and if it meets your requirements, you can use this ligand structure. If you encounter any other issues while using EDock, please feel free to contact me for further assistance.

Best wishes,
Wenyi

Hi Wenyi,
I have successfully submitted. Thank you so much.
Best wishes
Jinxian

Hi again, may I ask what XScore stands for? Thank you.

x-score (http://websites.umich.edu/~shaomengwang ... are/xtool/) is a scoring function used by EDock to rank different poses.