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 Post subject: selecting Hetatoms for simultaneously docking
PostPosted: Sat May 30, 2009 10:44 am 

Joined: Wed Apr 29, 2009 6:16 am
Posts: 2
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.


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 Post subject: Re: selecting Hetatoms for simultaneously docking
PostPosted: Tue Jun 02, 2009 7:43 pm 

Joined: Wed Oct 29, 2008 2:24 pm
Posts: 204
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.


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 Post subject: Re: selecting Hetatoms for simultaneously docking
PostPosted: Wed Oct 09, 2013 2:37 pm 

Joined: Wed Oct 09, 2013 1:56 pm
Posts: 2
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


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 Post subject: Re: selecting Hetatoms for simultaneously docking
PostPosted: Wed Oct 09, 2013 6:50 pm 

Joined: Wed Oct 29, 2008 2:24 pm
Posts: 204
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


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 Post subject: Re: selecting Hetatoms for simultaneously docking
PostPosted: Tue Oct 15, 2013 12:22 pm 

Joined: Wed Oct 09, 2013 1:56 pm
Posts: 2
bikadi wrote:
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.


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 Post subject: Re: selecting Hetatoms for simultaneously docking
PostPosted: Wed Oct 16, 2013 6:26 pm 

Joined: Wed Oct 29, 2008 2:24 pm
Posts: 204
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


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