[AMBER] problem of the protonation of the ligand

From: Enrico Martinez via AMBER <amber.ambermd.org>
Date: Fri, 2 Sep 2022 18:57:33 +0200

Dear Amber Users!
I've just noticed a bug related to the preparation of the ligand for
md simulation.
In fact, on the step of the adding hydrogens via babel,
obabel lig_withoutH.pdb -O lig_withH.pdb -h

depending on the initial structure of the ligand, sometimes some extra
hydrogens are added resulting in wrong geometry of the compound. After
that antechamber could not generate input parameters for such
compounds. Would it be possible to add hydrogens to the ligand in
another way to avoid such issue or alternatively to use some option
for open-babel to check the output ?
Many thanks in advance

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Received on Fri Sep 02 2022 - 10:00:04 PDT
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