[gmx-users] Writing PDB file so that protonation state of HIS is explicit by name

[Mark Abraham]

Hi,

The name that is output comes directly from the file that is passed to -s,
so you should arrange for that file to have the name you want, eg. through
how you made the tpr file.

Mark

On Mon, Apr 23, 2018, 17:23 Dawid das <addiw7 at googlemail.com> wrote:

> So they were. How should I modify my trjconv command to get this effect?
> Because with
>
> gmx trjconv -f npt-md-prod-center.xtc -o npt-md-prod-3ns.pdb -pbc mol
> -center -s npt-md-prod.tpr -ndec 6 -tu ns -b 3 -e 3
>
> I don't and I don't really see this option when calling gmx trjconv -h.
>
> 2018-04-23 17:18 GMT+02:00 Justin Lemkul <jalemkul at vt.edu>:
>
> >
> >
> > On 4/23/18 11:15 AM, Dawid das wrote:
> >
> >> Dear All,
> >>
> >> Is it possible to create PDB file from XTC so that naming of histidine
> >> residues
> >> is HSE, HSD, HSP instead of HIS?
> >>
> >
> > Yes, but only if they were named as such in the topology and therefore in
> > the .tpr file being used to do the conversion.
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Assistant Professor
> > Virginia Tech Department of Biochemistry
> >
> > 303 Engel Hall
> > 340 West Campus Dr.
> > Blacksburg, VA 24061
> >
> > jalemkul at vt.edu | (540) 231-3129
> > http://www.thelemkullab.com
> >
> > ==================================================
> >
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