[gmx-users] HIS as HID or HIE

[Quyen V. Vu]

I have done simulation that have HIS in binding site, so I run 2 simulation
one with HIE and the other is HID and then I will check is there any
difference (hydrogen bond) between 2 simulations and then decide which
protonation state of HIS should be employed. You can try in that way

On Thu, Jul 5, 2018, 19:57 Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/5/18 8:50 AM, antonia vyrkou wrote:
> > Hello,
> >
> >
> >
> > I am using GROMACS 5.1.4 and while trying to convert a .pdb file to .gro
> I
> > get the error message
> >
> > “Fatal error:
> >
> > Atom HD1 in residue HIS 66 was not found in rtp entry HIE with 17 atoms
> >
> > while sorting atoms.”
> >
> > Is it not possible to treat some HIS molecules as HID  (where HD1 exists)
> > and dome as HIE (instead of HD1 there is HE2)?
>
> Choose the protonation state interactively with the -his option of
> pdb2gmx, but note that your structure will have to be stripped of H
> atoms with -ignh if you are changing the protonation state, otherwise
> you'll just end up with the same fatal error.
>
> -Justin
>
> --
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>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
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