Re: [Apbs-users] Grid settings...

[Nathan B. <ba...@cc...>]

Hello again --

Please see the comments below:

> I want to calculate the POLAR and APOLAR contributions to solvation =20=

> energies for two lagre proteins and a complex of both to estimate =20
> the binding energy between them (this in order to asses the effec of =20=

> a puntual mutation on one of then to the binding energy). But I read =20=

> on the APBS user's guide and/or in some tutorial that for this kind =20=

> of calculations (solvation enegies and binding energies) the exact =20
> same grid deffinitios must be used for all the molecules, does this =20=

> means that I should generate a big grid fo my protein complex

That is the most "stable" approach (e.g., least sensitive to grid =20
spacing)...

> and then unse the same grid for each of the proteins alone, or can I =20=

> define a grid for ecah protein and the complex but mantaining the =20
> grid resolution (A/grid_point)?

...but you can use this approach as well if you are sure the solvation =20=

energies you're calculating are converged with respect to grid spacing.

> Should these be a MG-auto or an MG-manual calculation ?

mg-auto is probably best.

> Is the size of  the grid relevant or just the resolution in order to =20=

> have cualitative results?

Both, since too small of a grid extent can lead to artifacts from the =20=

boundary condition approximations.  I'd recommend using psize.py or =20
PDB2PQR on the complex to get your cglen/fglen values for the complex.

-- Nathan

>
> Thanks
>
> Ra=FAl Araya-Secchi
> =
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--
Associate Professor, Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology, Washington University in St. Louis
Web: http://cholla.wustl.edu/