[gmx-users] to neutralize the system

[Alexander Alexander]

Hello Mark,

I still need help choosing the right method of neutralization of my system.
I am wondering how the final states of the surface-binding process can shed
light on choosing the feasible method of neutralization, here, either
protonation (deprotonation) of amino acid and peptide or adding ions Na+
(Cl-)?

For example, in one sample, I neutralized the Glutamic(zwitterionic form)
by protonating it and then in simulation, it gradually absorbed firstly to
the surface via one of the Hydrogen(C-H) in the end of the side chain, and
then laid steady down while NH3 group was pointing up.
In another sample, again I neutralized the Arginine(zwitterionic form) by
deprotonating it and then in simulation, it absorbed firstly to the surface
via the COO(-) group in the backbone, and then laid steady down similar to
the Glutamic.

Many thanks in advance.
Regards,
Alex



On Wed, Jun 15, 2016 at 12:28 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> So you need to choose a topology for the amino acid that is consistent with
> the end states of the surface-binding process (whatever that is). This
> drives the answer to the question of what methods for neutralization are
> feasible.
>
> Mark
>
> On Wed, Jun 15, 2016 at 12:06 PM Alexander Alexander <
> alexanderwien2k at gmail.com> wrote:
>
> > Hello,
> >
> > The final goal is to model the adsorption behavior of a heptapeptide to a
> > metal surface, and meanwhile, calculation of the single amino
> acid(involved
> > in the peptide) binding free energy into the same surface.
> > Some of the residues of amino acid are charged, however, their charge
> would
> > get cancel out (sometime) each other when they come together in the
> > heptapeptide.
> >
> > Thanks,
> > Regards,
> > Alex
> >
> > On Wed, Jun 15, 2016 at 11:47 AM, Mark Abraham <mark.j.abraham at gmail.com
> >
> > wrote:
> >
> > > Hi,
> > >
> > > Such an answer starts with "what are you trying to model?"
> > >
> > > Mark
> > >
> > > On Wed, Jun 15, 2016 at 11:45 AM Alexander Alexander <
> > > alexanderwien2k at gmail.com> wrote:
> > >
> > > > Hello,
> > > >
> > > > How about neutralization of these cases, a single amino acid
> > > (zwitterionic
> > > > form)
> > > >  or a peptide in aqueous solution;
> > > > I was wondering which of below methods is preferable for neutralizing
> > the
> > > > system?
> > > > One is the introducing a counter-ion(Na or Cl for example) and the
> > second
> > > > one is the  protonation(or deprotonaton) the amino acid or peptide by
> > > > adding or removing one Hydrogen atom, so,
> > > >
> > > > Thanks,
> > > > Regards,
> > > > Alex
> > > >
> > > > On Wed, Jun 15, 2016 at 8:47 AM, Groenhof, Gerrit <ggroenh at gwdg.de>
> > > wrote:
> > > >
> > > > > You always need to neutralise with counter-ion, rather than rely on
> > the
> > > > > uniform background charge that the PME method introduces if your
> > system
> > > > is
> > > > > charged. The background charge introduces artefacts for
> > non-homogeneous
> > > > > systems by placing charge uniformly across the system rather than
> > > inside
> > > > > the higher dielectric. For further explanation and quantification
> of
> > > the
> > > > > artifact see the paper by Hub et al:
> > > > > http://pubs.acs.org/doi/abs/10.1021/ct400626b
> > > > >
> > > > > Gerrit
> > > > >
> > > > >
> > > > > Message: 4
> > > > > Date: Wed, 15 Jun 2016 01:00:40 +0300
> > > > > From: Qasim Pars <qasimpars at gmail.com>
> > > > > To: gmx-users at gromacs.org
> > > > > Subject: [gmx-users] to neutralize the system
> > > > > Message-ID:
> > > > >         <
> > > > > CAGQgkdSgAweitZmGxMj10p7HcVAzAdqnTc7evJOzPXhmyhmo5A at mail.gmail.com
> >
> > > > > Content-Type: text/plain; charset=UTF-8
> > > > >
> > > > > Dear gmx users,
> > > > >
> > > > > I am confused on below questions:
> > > > >
> > > > > 1) Is it necessary to neutralize a protein without ligand?  Does
> the
> > > PME
> > > > > method work with a charged protein correctly?
> > > > >
> > > > > 2) I have done lots of MD simulations at a charged complex
> structure
> > > > > (protein+ligand) with the PME method using GROMACS. I haven't come
> > > across
> > > > > with any problems because of the charge of the system. It means
> that
> > > the
> > > > > PME method works at a charged complex system properly. In spite of
> > > that,
> > > > do
> > > > > you think that I need to neutralize a charged complex system?
> > > > >
> > > > > Can anyone comment on above questions?
> > > > >
> > > > > Cheers,
> > > > >
> > > > > --
> > > > > Qasim Pars
> > > > >
> > > > >
> > > > > ------------------------------
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