[AMBER] How to protonate ligand manually ?

From: Enrico Martinez via AMBER <amber.ambermd.org>
Date: Mon, 13 Feb 2023 11:03:27 +0100

Dear Amber Users!

I am preparing protein-ligand system using an X-ray structure which has not
any information about coordinates of hydrogen atoms.

How could I add manually protons to the ligand molecule (e.g. selecting
atoms that should be protonates etc ..) in the case if software like
open-babel or reduce can not protonate small molecule in a correct way ?

Many thanks in advance

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Received on Mon Feb 13 2023 - 02:30:03 PST
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