[gmx-users] Adding hydrogen atom to specific Glu/Asp carboxyl oxygen atom

[Dawid das]

Yes, I have already figure that out, thanks ;). I have simply exchanged OE1
and OE2 atoms names and translated HE2 atom by vector between OE1 and OE2
in *gro file. Also I exchanged OE1 and OE2 atom names in *top file.

Best regards,
Dawid Grabarek

2016-11-09 12:56 GMT+01:00 Dd H <ddhecnu at gmail.com>:

> Exchange their atom names？
>
> Dading Huang
>
> On Wed, Nov 9, 2016 at 7:23 PM, Dawid das <addiw7 at googlemail.com> wrote:
>
> > Dear Gromacs Experts,
> >
> > I know how to specify which Glu/Asp residues are to be
> > protonated/deprotonated with
> > pdb2gmx tool. However, I do not like that the hydrogen is added to one of
> > the oxygen atoms
> > of carboxyl moiety. I would like it to be found on the other oxygen. Is
> > there any other way
> > except modifying the *top file by hand?
> >
> > Best regards,
> > Dawid
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