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From: Irene Newhouse (einew_at_hotmail.com)
Date: Mon Jan 11 2010 - 16:20:50 CST

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?

 

Thanks!

Irene Newhouse
                                               
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