[gmx-users] Zn moves away from protein - ligand complex

[HongTham]

HI Mark,
I don't get the reason why this happens to Zn since Protein and ligand are
fix well with trjconv options.
Would you please point to me particular reason for it? is it simply because
of visualization or there is really problem with simulation?

Thank you very much
Hongtham

On Mon, Apr 18, 2016 at 9:35 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> If you have a cluster of things that make sense to treat together then you
> must tell the tool that, via using such an index group. We haven't yet
> worked out to implement "do what I want" :-)
>
> Mark
>
> On Mon, 18 Apr 2016 13:40 HongTham <hongtham0709 at gmail.com> wrote:
>
> > Hello Gromacs users,
> > I'm running a Zn bound protein - ligand complex simulation. I solvated
> > whole system in a dodecahedron box. I also meet the problems with
> boundary
> > effects. I try to use the gmx trjconv with option -pbc mol -ur compact
> > -center to fix the problem. However, it doesn't work. The protein and
> > ligand was centered to the water box, but not Zn ion.
> > In some frame, Zn stay in the active site, sometime, it appear out site
> of
> > the active site. I use VMD and display the system with many box (not only
> > one unit), and see ZN till stay in the active site, but that is Zn of
> > neighbor box, not the current box. its Zn ion now is stay in the active
> > site of another box.
> > I also tried with many option (cluster, nojump, -fit rot+trans) or change
> > the selection of centering but they all useless. The -pbc nojump seems to
> > be fine , it makes the protein + ligand + Zn stay together, but the water
> > molecules are definitely distracted. It is difficult for me to calculate
> > the water molecules within 0.5 to 10 nm of Zn and ligand.
> > Anyone has been same situation with me? Would anyone give me a suggestion
> > to fix that problem.
> > Thank you so much.
> > Best regards,
> > Hongtham
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