Re: [AMBER] formal charge of the ligand

From: Mary Varughese <>
Date: Sat, 28 Jun 2014 11:43:21 +0530


Infact i tried MD simulation with three nucleic acid sequences. I
assigned a -1 charge (COO-)(chimera also gives -1) in the assumption
that under physiological condition it will most probably assume COO-
state. The binding seems to be stable. but on MMPBSA calculation
PBtotal = -5.8 and TdeltaS= -17.8. What do you think about the result.
Is this not a possible binding. Should i neglect the entropy part.
 the ligand actually binds in the experiments. ( its not caffeic acid
but another ligand including COOH group)
Its at this point i doubt the appropriateness of -ve charge.
Is it normal to take 0 charge with COOH? i asked similar reference to
compare the result obtained in mmpbsa with charged ligands.

I am really in need of your's suggestions.

Thank you very much for the valuable suggestions.

Mary Varughese

On 6/27/14, Soumendranath Bhakat <> wrote:
> 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

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Received on Fri Jun 27 2014 - 23:30:02 PDT
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