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Unwanted hydrogen on azide group in ligand
https://www.dockingserver.com/forum/viewtopic.php?f=3&t=172
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Author:  monisha92 [ Tue Mar 28, 2017 7:53 pm ]
Post subject:  Unwanted hydrogen on azide group in ligand

Hi all,
I have a ligand with azide group. Every time I draw or upload the ligand, after computing it is taking itself one hydrogen at the negative end of azide group. According to the resonance forms of azide group, there must be one negatively charged and another positively charged nitrogen but I don't want hydrogen on the negatively charged nitrogen.

Can anyone help me why it is happening and how to fix this problem?

Thanks in advance.

Author:  bikadi [ Wed Mar 29, 2017 8:57 pm ]
Post subject:  Re: Unwanted hydrogen on azide group in ligand

You can uncheck the pH button or change the pH

Author:  monisha92 [ Thu Mar 30, 2017 1:10 pm ]
Post subject:  Re: Unwanted hydrogen on azide group in ligand

bikadi wrote:
You can uncheck the pH button or change the pH

It didn't help. It is protonated irrespective of the pH value. Also did by unchecking the pH button.

Author:  bikadi [ Mon Apr 03, 2017 7:17 pm ]
Post subject:  Re: Unwanted hydrogen on azide group in ligand

Try uploading an optimized ligand and choose optimization none option.

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