Dear modeller users,

I incorrectly wrote, "However, this is not the case after optimization (the single charge has a higher energy value)" in my previous mail. This should have been "the single charge has a lower energy value."

Sorry about the inconvenience, Abdullah From: abdullah_renk_ahmed@hotmail.com To: modeller_usage@salilab.org; andrey.kajava@crbm.cnrs.fr Subject: coulomb energy Date: Mon, 19 Apr 2010 16:11:58 +0600

Dear Modeller users,

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")

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

Thank you in advance for your reply, Abdullah Ahmed Hotmail: Free, trusted and rich email service. Get it now. Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. Sign up now. _________________________________________________________________ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. https://signup.live.com/signup.aspx?id=60969