AMBER Archive (2008)

Subject: Re: AMBER: Electrostatic Energy Components

From: Junmei Wang (junmwang_at_gmail.com)
Date: Sun Nov 23 2008 - 21:36:38 CST

Hi everyone,

I am sorry I didn't follow the discussion about how gaff derives its
torsional angle terms. Here is my clarification: the gaff torsional angle
terms were developed to make the whole MM energies (including bond length,
bond angle, torsional, and all non-bonded terms) reproduce the QM energies.
Here, a MM or QM energy is the relative energy between two conformations.
Both systematic search and a genetic algorithm were applied to do the
optimizations. The details were presented in the GAFF paper (JCC, 25,
1157-1174 ) and our Parmscan paper (JCC, 22, 1219-1228). I am sorry some
sentences in the paper are misleading.

Best regards

Junmei

On Fri, Nov 21, 2008 at 1:29 PM, <guardiani_at_fi.infn.it> wrote:

> 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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