Re: [Apbs-users] How to get the values of electrostatic potential for all the coordinates in a pqr file a time?

[Nathan B. <nat...@wu...>]

Hello --

You could modify the tools/mesh/value.c file to read the potential
from several places.  This code was intended to be a template.  Note
that you can't use the values from a single calculation beacuse they
contain self-interaction terms.  Instead, you will need to (1) perform
a calculation with the desired inhomogeneous dielectric, (2) perform a
calculation with a homogeneous dielectric with both the solvent and
solute dielectric values set to epsp from the previous calculation,
(3) subtract the results of (1) and (2), and (4) add in coulombic
interactions, scaled by the internal (epsp) dielectric coefficient.

Note that, if you compiled the Python wrappers, you can do this via
the Vgrid Python wrapper as well.  I'm Cc'ing some local folks who can
provide additional input.

Thanks,

Nathan

On 6/3/06, g_y...@st... <g_y...@st...> wrote:
> Hello,
>    I want to calculate proteins' electrostatic potential and get the
> value of electrostatic potential of every atom in the pqr files. I know
> tool/mesh/value may do that. But the tool only get one value a time
> from dx file. It is not suitable when dealing all the atoms in a
> protein especially for batch-dealing many proteins. Maybe output of
> finite element dx file can achieve this goal, but the default dx file
> is multigrid. Who knows how to get the values of electrostatic
> potential for all the coordinates in a pqr file a time by APBS.
> Anyone's advice will be appreciated.
>
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-- 
Assistant Professor, Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology, Washington University in St. Louis
Web: http://cholla.wustl.edu/