Hi Marc -
What are the grid spacings or lengths of the fine mesh?
Pacific Northwest National Laboratory
From: Marc van der Kamp [mailto:marcvanderkamp@...]
Sent: Friday, June 03, 2011 4:13 AM
Subject: Re: [Apbs-users] Essentially no electrostatic potential for extreme upper and lower parts of solute?
It appears the mailing list didn't like the size of my email, so I'm sending it again without the tmp2.png and protein.pqr files.
---------- Forwarded message ----------
From: Marc van der Kamp <marcvanderkamp@...<mailto:marcvanderkamp@...>>
Date: 3 June 2011 12:08
Subject: Essentially no electrostatic potential for extreme upper and lower parts of solute?
I'm using APBS for the first time to visualize the surface potential of a protein in VMD. I've followed the instructions on http://www.poissonboltzmann.org/apbs/examples/visualization/apbs-electrostatics-in-vmd
This works, but it turns out that part of the molecule appears to be 'left out' of the electrostatic potential (so it isn't really colored, even with setting the scale data range to -10 and 10) - see for example the attached figure (tmp2.png).
Even when I change the scale data range to -1 and 1, the extreme parts of my protein are white (see tmp3.png).
This can't be realistic, can it?
I'm using freshly installed APBS 1.3 and VMD 1.8.7 (on Windows XP).
I checked the default mesh length settings in the APBS Tool plugin, which clearly encompasses the dimensions of my solute:
solute dimensions: 53.836 x 78.721 x 56.424
coarse and fine mesh lengths are roughly 81 by 118 by 85.
When I check the output (io.mc<http://io.mc>), I read the following:
solute dimensions = 56.878 x 81.841 x 59.532
Grid lengths = (66.616, 91.501, 69.204)
Grid lower corner = (8.641, 8.9, 8.873)
The mimimum coordinate values of my solute are about 15 for x,y,z.
So this appears to be fine too, I think.
As far as I can see, there is no problem with the .pqr file (created by "python ~/pdb2pqr/pdb2pqr.py --ff=amber protein.pdb protein.pqr"), i.e. all the atoms carry the expected charges.
What could be going wrong? And how could I solve it?
(I tried increasing the mesh lengths to something much larger than my solute, namely 100 by 160 by 100, with essentially the same results. )
I've attached io.mc<http://io.mc> and protein.pqr.
Many thanks in advance (and let me know if more info is needed)