[Users-list] Hydrophobic potential calculation

[Paolo Benedetti]

Hua Wong wrote:
> Well. I've begin fumbling with the grid packages. I am not using the  
> GUI because I wish to learn how to use Grid and automatize some  
> operations too...
> 
> I wish to do a hydrophobic potential calculation similar to that...
> http://biop.ox.ac.uk/www/lj2000/noble/noble_02.html
> 
> Can I have a hint about the important parameters I should set in  grid.in?

I'm sure you'll find a lot of hints reading the manual... For example:

"Chapter 16. Computing the hydrophobic energies" (page 93)

or

"Chapter 49. Greater tutorial 02
HYDROPHOBIC Molecular Interaction Field"  (page 455)


> Do I have to use the DRY probe?

from Chapter 16, see page 97:
"The name of the hydrophobic Probe is DRY"

> Most importantly, is there a size limitation for the system?
> I tried with a small part and it seems to run, while the whole system  
> (roughly 8000 atoms) returns me the D475-E message...
> 
> Is there a way I can get around this problem?

Again, one could have a look to manual at page 312 :

39.2.48. D475-E (D475-E) NUMBER OF Y PLANES TOO LARGE

  The grid points are arranged in planes which are perpendicular to the 
x, y and z axes, and the computation is performed on a single "z-plane" 
of grid points at a time; i.e. on points in a plane perpendicular to the 
z-axis.
  Any number of z-planes may be computed one after another, as specified 
by NZ1 and NZ2 (See Index under "NZ1 and NZ2"). However, the number of 
planes perpendicular to the y-axis (the "y-planes") is limited to 199. 
The number of x-planes is similarly limited to 199 (See below).
  It may help to reorient a long macromolecule with its long axis 
parallel to z. Alternatively TOPX, BOTX, etc, etc may be used to 
restrict the size of the computation. More often, however, the problem 
lies with an inappropriate value for directive NPLA.


We do not think that manual we wrote can solve any problems, but at 
least it is a good starting point.

Regards,
Paolo

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