[AMBER] Inconsistent Internal energy from monomer to dimer

From: Josep Maria Campanera Alsina <campaxic.gmail.com>
Date: Tue, 3 Apr 2012 13:15:55 +0200

Dear all,

I have found an inconsistency in MMGBSA/PBSA calculations that
embittering me. This is about the internal INT term (BOND+ ANGLES
+DIHEDRALS) in the MMGSBA decomposition only. A colleague has passed
to me two simulations run apparently under the same conditions in
AMBER11. One simulation consists of a peptide of 26 residues (408
atoms) and the other one a dimer of the SAME peptide with 52 residues
(816 atoms), the double of the same atoms. I've run the MMGBSA
analysis (AMBER11 perl and python scripts) and the INT term
(BOND+ANGLE+DIHED) of the DIMER (1135.89 kcal/mol) is not, by far, the
double of the INT term of the MONOMER (545.67 kcal/mol). I would just
expect approximately a double value. Actually, there is a difference
of 22 kcal/mol (1135.89/2-545.67)!!!!!!!!

Here is my question, How can be that the internal energy per monomer
unit changes so much? I think it cannot be! BOND, ANGLES AND DIHED
cannot be so different in both systems, actually should be very
similar in terms of monomer units. I've been trying a lot of things
(topology files, amber inputs etc.) to correct this but I haven't
found anything strange, neither in the dynamics nor in the MMGBSA!
What do you think? Is this energy values normal? What's wrong here?
Where should I focus?

All comments will be welcome.

Josep M.,

PD: Find attached amber files for inspection.


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Received on Tue Apr 03 2012 - 04:30:04 PDT
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