Re: [AMBER] formal charge of the ligand

From: Jason Swails <>
Date: Fri, 27 Jun 2014 09:52:36 -0400

On Fri, 2014-06-27 at 18:03 +0530, Soumendranath Bhakat wrote:
> Hi Mary, To further jasons explanation you can easily check the
> protonation state in chimera. Just upload the ligand in chimera go to
> DockPrep and in add charge part use AM1-BCC charge and you will get
> exact protonation state either positive or negative and then run
> antechamber with nc 'charge' it will create parameter.

Do you know how Chimera assigns protonation states? If not, you have no
reason to trust its assignments. See the "Add Hydrogens" command
description for the Chimera manual:

Note in particular the following disclaimer: The resulting protonation
states of such groups and of those with possibly perturbed pKa values
(for example, in active sites or coordinating metal ions) should be
checked manually and corrected as needed.

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Fri Jun 27 2014 - 07:00:02 PDT
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