Re: [modeller_usage] coulomb energy

[Modeller Caretaker <>]

On 04/19/2010 03:11 AM, abdullah ahmed wrote:
> I am working on two structures where the insides of the structure do not
> have access to water.
> One structure contains a charged Lysine and a charged Glutamic acid
> residue facing each other, with distances favorable for electrostatic
> interactions.
> The other contains a negatively charged residue only.
> There are no other charges in either molecule, but there are a large
> number of Glutamines. The dielectric constant is set to 1.
>
> Theoretically, the structure with two opposite charges should have a
> higher coulomb energy. However, this is not the case after optimization
> (the single charge has a higher energy value).
>
> I would like to know if this is because:
>
> 1) I haven't used the coloumb energies properly? (I used the following
> line in the optimization.py script to switch it on:
> "env.edat.dynamic_coulomb= True")

That sounds fine. Note, however, that this will calculate electrostatic 
interactions for the whole protein, so a local favorable interaction may 
be canceled out by other interactions in the protein.

> 2) Modeller calculates the electrostatic energies in a different way to
> what I has excepting?

It's plain old inverse square with a constant dielectric and a force 
switch. You might want to check the charges on your residues of 
interest, however - since we don't generally use electrostatics in 
comparative modeling the charges have not been exhaustively parameterized.

	Ben Webb, Modeller Caretaker
--
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