[gmx-users] Calculating electric potential in Gromacs

[Nathan C. Rockwell]

We recently did something similar with MEAD to estimate pKa for a
protein
and found it necessary to average over several snapshots, because slight
positional changes in MD translated into bigger changes in electrostatic
properties. 

Both MEAD and APBS require a PQR file as input (replaces the B and
occupancy
with radius and charge). editconf can make a PQR file for you (-mead)
from a
.tpr file, but the radii (especially for H) are usually much smaller for
MD
than is recommended for electrostatics calculations, so you will
probably
need to do some hacking. The charges from your MD force field are
probably
OK for electrostatics, and in fact I would recommend keeping them
because
that will give results that are closer to the internal electrostatics.

Alternately, newer versions of VMD include a PME calculator which might
help, but I don't know if that is tied to protein structure.

Hope that helps,
Nathan Rockwell



 

On 11/4/05 12:53 PM, "diego vallejo" <diego.vallejo at gmail.com> wrote:

> you can
> 1.extract a pdb file,
> 2. use a std electrostactic calculation package: APBS for instance
(FDPB
> model)
> 
> is that what u need?
> 
> saludos
> Diego Vallejo
> 
> 
> At 05:22 p.m. 04/11/2005, you wrote:
> 
>> On Fri, 2005-11-04 at 15:07 -0500, Bob Johnson wrote:
>>> Hello everyone,
>>> Is there anyway to calculate the electric potential in Gromacs. I am
using
>>> particle mesh ewald which, in my understanding, calculates the
electric
>>> potential on a grid and interpolates between the grid points. Is
there
>> a way to
>>> extract this information?
>>> 
>>> My system consists of ssDNA and a carbon nanotube. I would like to
>> calculate the
>>> electric potential at the surface of the nanotube upon adsorption of
ssDNA.
>>> 
>> Not without some programming I'm afraid.
>> 
>>> Thanks,
>>> Bob Johnson
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>> David.
>>
________________________________________________________________________
>> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
>> Dept. of Cell and Molecular Biology, Uppsala University.
>> Husargatan 3, Box 596,          75124 Uppsala, Sweden
>> phone:  46 18 471 4205          fax: 46 18 511 755
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http://xray.bmc.uu.se/~spoel
>>
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>