VMD-L Mailing List

From: Jan Saam (jan.saam_at_charite.de)
Date: Fri Sep 12 2003 - 04:42:09 CDT

Scott,

take a look at
http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/pbcwrap/
where you'll find a VMD-script.
I once wrote it to wrap atoms that diffused out of the original unit
cell back into the cell using the cell geometry in the *.xst file.
This works for NAMD and I guess that AMBER has a similar cell geometry
file. You can probably easily adapt the script to read that file.

I understand that you actually want to de-wrap your trajectory: Your
ligand seems to be near the cell boundary and eventually gets wrapped to
the other side of the cell. Right?
This could also be fixed with the script if you adapt it accordingly.
You basically have to change the sign of the translocation vector.
The script currently detects when the specified selection leaves the
boundaries and wraps the atoms accordingly. You must change it in a way
that you specify manually for which frames you want your ligand to be
dewrapped.

Hope that helps,
                Jan

Am Don, 2003-09-11 um 22.07 schrieb Scott Stagg:
> I am trying to make a movie of my simulation where in each frame the
> protein is superposed back on the first frame. No problem there except
> that in some frames a ligand that is bound to the protein is wrapped
> around the periodic boundary while the protein is not. So in the movie,
> it looks like every so often the ligand jumps off the protein. Is there
> any way to get that molecule back in its proper place?It is a constant
> pressure simulation, so the box size changes, which I would imagine
> makes it hard to wrap the ligand back around. Any suggestions?
>
> Thanks,
> Scott Stagg
>