VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Jan 11 2010 - 16:59:59 CST

On Mon, Jan 11, 2010 at 5:20 PM, Irene Newhouse <einew_at_hotmail.com> wrote:
> I just ran PME electrostatics for the first time.
>
> After loading my traj, I used the RMSD traj tool to align the frames. Then,
> from the PME controls, I selected 'choose charges from CHARMM parameters'. A
> copy of the parameter file is in the dir. from which I'm running. I selected
> the cell from VMD info; it looked very similar to the .xsc file, so I left
> it there. I did not select 'allow unaligned cells'.I left the resolution,
> etc. parameters alone. I sellected 'all' for avg. frames. I selected 'update
> selection for each frame'.  I entered a name for the dx file. I chose 'load
> into' new. I chose isosurface.
>
> The isosurfaces appear wrapped & are offset from the protein. What am I
> missing, please?

the proper origin?

axel.

>
> Thanks!
> Irene Newhouse
>
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-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.