The enzyme has a co-factor. I want to dock the substrate to the same cavity with the co-factor simultaneously. How should I Select simulation box ( and select Hetatoms!) to prepare the protein for docking? Any help will be appreciated. Thanks.

Simply select the co-factor in the protein clean page in the select hetatoms box (if the cofactor is heme, it is automatically selected), then it will be involved in docking.

Hello, I have the same problem. I need a cofactor for my docking. So I tried to choose it in heteroatom box in clean protein page...late I use this protein for docking but I didn't see my cofactor in docking results (section reference ligands contains only ligand that should be deleted, no cofactor). Please can you give me an advise? Thank you

Could you please send me a link to your calculation? It is possible that the cofactor is there just you cannot see it so I should check this first.

Thanks,
Zsolt

Thank you for your quick response. I try it again and better:-) But I still don't see the cofactor...Here is the link to my calculation (http://www.dockingserver.com/web/docking/210949/). I registered, so I don't know if you can see it. I'm really beginer, so i don't know if my results are ok. Thank you.

Hi,

the NAPD is there in the docked structure but it is very far away from the simulation box you used for docking.

Best Regards,
Zsolt