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