Re: [ccp4bb]: Grasp/electrostatic surface

[Norbert Straeter <strater@chemie.fu-berlin.de>]

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Dear Phil,

as also stated by the authors, GRASP should not be used for the
calculation of electrostatic potentials for large molecules.
As the manual states:

>Grasp includes a Poisson- Boltzmann (PB) solver which is a similar but
>simpler version of that used by DelPhi. The fields calculated by it are
>for qualitative use only. For quantitative use there is full support for
>the output from DelPhi, in terms of potential maps, dielectric maps,
>modified pdb files, charge files, size files, etc.

That is indeed true. I once calculated the potential for a hexameric
molecule with GRASP and the potential map showed significant deviations
from the symmetry whereas the map calculated with Delphi did not.
Unfortunately Delphi (from the same lab as Grasp) costs US $250.
(http://trantor.bioc.columbia.edu/delphi/)

An alternative maybe MEAD, which is freely available from 
http://www.scripps.edu/bashford/ and can be used to color surfaces e.g. by
Dino (http://www.biozentrum.unibas.ch/~xray/dino/). As far as I remember
both programs are not very straightforward to use.

-Norbert


> > I'm trying to calculate an electrostaic potential surface, and Grasp
> seems not to take more than about 13100 atoms. is there any way of
> increasing this? Or are there other programs which will calculate an
> electrostatic surface for large molecules?
> 
> 	      Phil
>