[gmx-users] An extra charge

[Mark Abraham]

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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