AMBER Archive (2008)

Subject: AMBER: Electrostatic Energy Components

From: guardiani_at_fi.infn.it
Date: Fri Nov 21 2008 - 13:29:08 CST

Dear Amber experts,

I would like to ask a question that probably you will
consider trivial. What is the difference between the
energy components 1-4 EEL and EELEC ?

I am performing REMD simulations in implicit solvent
(igb=7) on a number of peptides. As I understand EGB
represents the electrostatic component of the energy
of interaction with the solvent while EEL 1-4 and
EELEC refer to the intramolecular interaction energy.
Why is this energy split in two components? Why is
the EEL 1-4 term usually positive while EELEC is
generally negative ? I noticed that there is a sort of
compensation between EELEC and EGB, that is the peptides
with lower EELEC have higher EGB and vice-versa.
I interpreted this correlation by assuming that,
if a residue interact strongly with other residues in the
protein, it cannot interact as strongly with the solvent.
Is my interpretation correct?

I also noticed that if I add together EEL 1-4 and EELEC,
this correlation with EGB becomes weaker. Why is it so?
I ask you this question because in my work, I started with
a free peptide and then I created a number of variants
closed with disulfide bonds placed in different positions.
Which quantity is it better to use to study the intramolecular
electrostatic energy, EELEC or EELEC + EEL 1-4?

I thank you very much for your help and I am looking forward to
receiving feedback from you,

Carlo Guardiani

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