Re: [AMBER] formal charge of the ligand

From: Soumendranath Bhakat <>
Date: Fri, 27 Jun 2014 22:10:19 +0530

As per the ligand bound to active site such as for example caffeic
acid with C00- group Chimera will give a possible hint ofthe net
charge of the ligand. As in this case there is no active site charge
or metal ion so if the user extract the ligand from its bound
conformation and go to add charges which is within dockprep or even by
just clickig add charges chimera will run sleap assuming the system is
in physiological pH to calculate net charge of the ligand and after
saving the file by running antechamber in Chimera if user upload it
and run antechamber by mentiining nc as reported by Chimera it will
assign partial charges well. Assume user has no metal ion as a ligand
and they dont need charge of the active site then chimera assign
partial charges and hydrogens in good accordance. But if user knows
that there is coo- group then they can use any external programme like
mmv or maestro or ds to add hydrogen and assign charge as per
chemistry knowledge in physiiological pH but that will be a bit more
lengthy process for a small thing.

On 6/27/14, Jason Swails <> wrote:
> 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
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list

Thanks & Regards;
Soumendranath Bhakat
AMBER mailing list
Received on Fri Jun 27 2014 - 10:00:02 PDT
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