VMD-L Mailing List

From: Irene Newhouse (einew_at_hotmail.com)
Date: Mon Jan 11 2010 - 17:17:50 CST

Oh yeah....

 

Thanks!

 

Irene
 
> Date: Mon, 11 Jan 2010 17:59:59 -0500
> Subject: Re: vmd-l: PME isosurface not superimposed on protein
> From: akohlmey_at_gmail.com
> To: einew_at_hotmail.com
> CC: vmd-l_at_ks.uiuc.edu
>
> 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
> >
> > ________________________________
> > Hotmail: Powerful Free email with security by Microsoft. Get it now.
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> Institute for Computational Molecular Science
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
                                               
_________________________________________________________________
Hotmail: Trusted email with Microsoft’s powerful SPAM protection.
http://clk.atdmt.com/GBL/go/196390706/direct/01/