Molecular Docking Server

Ligand prepare
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Author:  jessietxaa [ Mon Feb 01, 2010 7:47 am ]
Post subject:  Ligand prepare

Hi There,

I am a new customer of docking server, and tried to the inhibitors with protein. I recently subscribed the use of dockingserver. It was supposed that .sdf format should work for docking. Following the instructions, I uploaded my inhibitors in SDF file to the ligands folder and my protein to the protein folder. When I started docking, I selected the inhibitor and it showed ligand prepare, and always showed computing and wait for user to input. When I clicked the "confirm", the ligand only showed the 2D structure. However, when I continue do the docking, there is some wrong message came out "such as wrong .pdbqt", and the docking could not be done. Please let me know how to prepare the inhibitor.sdf for the docking. Thanks.


Author:  bikadi [ Mon Feb 01, 2010 8:36 am ]
Post subject:  Re: Ligand prepare

Hi Jess,

sdf files should work, but uploading files always has a higher risk of error than preparing everything within DockingServer. I have checked the error you've got - you are right, if there is no structure in the 3D box, it is a strong indication that something went wrong. Please follow this procedure to get a ligand ready for docking (I did the same and put the ligand called 'test' into your ligand directory):

- Click on the name of the problematic ligand
- Double click on the 2D image of the problematic ligand
- Select Edit -> Copy as smiles
- Go back to My ligands -> Draw ligand
- On the top of the drawing window, select Edit-> Paste
- Add a name to the ligand and save it
- Use the default settings and click on Confirm

This should work or alternatively you can use the ligand named 'test'.

Kind Regards,

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