[gmx-users] An extra charge

[Alexander Alexander]

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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