[gmx-users] pbc whole

[Tsjerk Wassenaar]

Hi Carla,

> I checked with genconf & now I'm certain that my ATP molecule is still with
> the protein

That's good to know :)

>>> trjconv -s a.tpr -f b.xtc -o c.xtc -center -ur compact -pbc mol
>>> (centering on "Protein")

So what did come out of this then? It should have given you a compact
representation of your system with the protein in the center. But if
the protein's in the center and everything is put as close to that
center as possible, which is what "compact" does, then the ATP should
be there too. Can you make an image of the last frame and send a link
to it? Alternatively, I have a patched version of trjconv that you can
use to do the trick. I can send it if you want.

Cheers,

Tsjerk


-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist