[gmx-users] An extra charge

[Alexander Alexander]

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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