[gmx-users] An extra charge

[Mark Abraham]

Hi,

None of this matters - you care about whether the force field was
parameterized to model a single-residue zwitterion, and papers looking and
side-chain analogues literally do not matter. Checkout the original
literature (which you should have done before choosing the force field!)

Mark

On Sat, Jun 11, 2016 at 9:14 PM Alexander Alexander <
alexanderwien2k at gmail.com> wrote:

> Hi,
>
> Unfortunately, most of the works on single amino acides which I have seen
> already focused somehow on amino acid side chains only, by truncating the
> amino acid in \alpha Carbon and removing the whole backbone, then no
> zwitterion issue in single amino acid comes up whatever force field are
> used, but, I want to consider the zwitterion form :-(  .
>
> Regards,
> Alex
>
> On Sat, Jun 11, 2016 at 8:50 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Hi,
> >
> > I don't know, but perhaps your background reading about your choice of
> > forcefield will prove informative about what has or has not been
> > parametrized or tested ;-)
> >
> > Mark
> >
> > On Sat, Jun 11, 2016 at 8:37 PM Alexander Alexander <
> > alexanderwien2k at gmail.com> wrote:
> >
> > > Hi,
> > >
> > > Yes, I am going to calculate the free energy of single amino acid (in
> > their
> > > zwitterion form) in water.
> > >
> > > I did not get your point, you mean that neither of them can not be used
> > for
> > > zwitterion form if the system is a single amino acid in water? Then
> how a
> > > single amino acid (in zwitterion form) can be treated here?
> > > Again, the second one works fine producing uncahrged single amino acid
> in
> > > zwitterion form.
> > > Thanks.
> > >
> > > Regards,
> > > Alex
> > >
> > > On Sat, Jun 11, 2016 at 8:20 PM, Mark Abraham <
> mark.j.abraham at gmail.com>
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > The zwitterion form modifies the alpha carbon charge, so can't be
> used
> > > > together for a single amino acid in this case. We should add a check
> > that
> > > > stops you running into this problem. It wasn't clear in your first
> post
> > > > that you were trying to get a topology for a single amino acid.
> > > >
> > > > Mark
> > > >
> > > > On Sat, Jun 11, 2016 at 7:49 PM Alexander Alexander <
> > > > alexanderwien2k at gmail.com> wrote:
> > > >
> > > > > Thanks for your response Mark.
> > > > >
> > > > > To keep the zwitterions form, two below possibilities are offered
> for
> > > > > terminies:
> > > > >
> > > > >  0: NH3+
> > > > >  1: ZWITTERION_NH3+ (only use with zwitterions containing exactly
> one
> > > > > residue)
> > > > >
> > > > > With "0:" the "-0.110 e" charge shows up while with "1:" it goes
> > fine,
> > > > but
> > > > > what the differences is? as stated, when there is just a single
> amino
> > > > acid
> > > > > in system, the second one should be chosen, and if more the first
> one
> > > > even
> > > > > if they are charged or uncharged.
> > > > >
> > > > > Best regards,
> > > > > Alex
> > > > >
> > > > > On Sat, Jun 11, 2016 at 7:23 PM, Mark Abraham <
> > > mark.j.abraham at gmail.com>
> > > > > wrote:
> > > > >
> > > > > > Hi,
> > > > > >
> > > > > > Look at your topology and consider where the charges go wrong.
> > > Probably
> > > > > > your termini selections are inappropriate.
> > > > > >
> > > > > > Mark
> > > > > >
> > > > > > On Sat, Jun 11, 2016 at 7:11 PM Alexander Alexander <
> > > > > > alexanderwien2k at gmail.com> wrote:
> > > > > >
> > > > > > > Dear gromacs user,
> > > > > > >
> > > > > > > I am expecting to get a uncharged GRO file of the Glutamic acid
> > by
> > > > > > invoking
> > > > > > > below command, and selecting the protonated version of it, but
> I
> > do
> > > > not
> > > > > > > know why I get unexpected total charge of "-0.110 e" at the end
> > > when
> > > > I
> > > > > > use
> > > > > > > the OPLS-AA force field while the other FF's result to the
> > expected
> > > > > > > uncharged one?
> > > > > > >
> > > > > > > ~> gmx pdb2gmx -f glu.pdb -o glu.gro -water tip3p -ignh -ter
> -glu
> > > > > > >
> > > > > > > OPLS-AA
> > > > > > >
> > > > > > > Protonated (charge 0) (GLUH)
> > > > > > >
> > > > > > > Total charge -0.110 e
> > > > > > >
> > > > > > > Any comment, please?
> > > > > > >
> > > > > > > Regards,
> > > > > > > Alex
> > > > > > > --
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