Coulomb 1-4 is only beteen the atoms that are 3 bonds away from each
other. The bonds prevent these atoms to get apart too far, so 1-4 won't
destabilize the overall structure. The SR part is negative, thus keeping
your protein together.
Gerrit
Message: 3
Date: Fri, 6 Mar 2009 19:43:19 +0900
From: Seungpyo Hong <sp1...@gmail.com>
Subject: [gmx-users] Positive energy for Coulumb term. Does this mean
Coulumb interaction destabilizes protein?
To: gmx-users@gromacs.org
Message-ID:
<bd5475eb0903060243q7a553766r70664758fa47f...@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
Dear GMX-Users,
As I analyze energy terms of proteins, I found something looks weird.
I thought that fullly folded proteins are stabilized by Coulomb interaction
(such as hydrogen bonds).
However, what I found embarasses me.
The Coulomb interaction seems to destabilize the protein structure as its
energy is positive.
Coul-SR + Coul-14 = 32 > 0
Coul-SR + Coul-14 + Coul-SR(Protein-Non-Protein) = 18 > 0
Energy Average RMSD Fluct. Drift
Tot-Drift
-------------------------------------------------------------------------------
Coul-SR:Protein-Protein -11.6253 365.244 357.507 -0.735925
-259.047
LJ-SR:Protein-Protein -6.51389 204.554 203.627 0.191426
67.3824
Coul-14:Protein-Protein 38.5848 1212.26 1196.75 1.90253
669.696
LJ-14:Protein-Protein 3.58465 112.688 112.645 -0.0303438
-10.6811
Coul-SR:Protein-Non-Protein -14.1247 443.927 437.195 -0.75795
-266.8
LJ-SR:Protein-Non-Protein -1.51471 47.6924 46.2568 -0.11429
-40.2302
I thought of the total charge of the protein; but it is only +2.
And, the structure is quite stable through the simulation. (RMSD: 0.17)
I am quite confusing about the effect of Coulumb interaction on the
stability of the protein.
I feel like I am missing very important concept about the stability of
protein or the energy term used here.
Can anyone help me to understand the effect of Coulumb interaction in the
stability of the protein?
Any opinion or comment would be great help for me.
Thank you very much!
Sincerely,
Seungpyo Hong
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