From: Kay Gottschalk <kay.gottschalk@ph...> - 2006-05-05 10:28:45
I want to calculate the angle between a water dipole and the field
line of a protein. Any idea how I might do that?
Dr. Kay-Eberhard Gottschalk
Applied Physics and Center for Nano Sciences
80799 Munich, Germany
Phone: +49-89-2180 3436
It shouldn't be too hard.
First, I would calculate the potential *in the absence of the water
molecule* and save the result as an OpenDX file.
Next, you can load this OpenDX data into a Vgrid object either using
the template code in apbs/tools/mesh/value.c or through Todd's
apbs/tools/python/vgrid/vgrid.py (assuming you compiled Python support
Finally, you can use the Vgrid object to evaluate the field at
specific points in space (e.g., the location of your water dipole).=20
This is demonstrated in the apbs/tools/mesh/value.c template code and
should be a reasonable starting point for your calculations.
Please let us know if you have any questions.
On 5/5/06, Kay Gottschalk <kay.gottschalk@...> wrote:
> Hi there,
> I want to calculate the angle between a water dipole and the field
> line of a protein. Any idea how I might do that?
> Dr. Kay-Eberhard Gottschalk
> Applied Physics and Center for Nano Sciences
> Ludwig-Maximilians University
> Amalienstr. 54
> 80799 Munich, Germany
> Phone: +49-89-2180 3436
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Assistant Professor, Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology, Washington University in St. Louis