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PostPosted: Mon Oct 05, 2009 11:06 am 
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Hi !!!!

Can anyone tell me is it possible to dock ligand with all hydrogen instead of polar Hydrogen by Autodock vina?

Thanks in advance.

Best Regards

Awantika Shrivastava


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PostPosted: Tue Oct 06, 2009 12:53 am 
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Hi Awantika,

The scoring function used in Vina is united-atom, i.e. it depends on the position of the heavy atoms only, so I'm not sure what purpose docking a fully protonated ligand would serve. Hydrogens are used only to type some heavy atoms, i.e. to decide if they are H-bond donors or acceptors. So, in short: "no".

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