AMBER Archive (2005)

Subject: AMBER: E of amber calculations

From: YoungJin Cho (young.j.cho_at_vanderbilt.edu)
Date: Wed Dec 14 2005 - 11:34:47 CST

Hi,
I'd better ask than being confused longer.
My question is about energy in amber calculations.
In the DNA tutorial, It shows the polyA-polyT decamer.
In comparison with starting B and A form DNA (the tutorials shows how
it changes from A to B in a water box), my question is from .out files.
At the beginning, from the fist minimazation (A form), energy changes
from -2.8014E+04 to -4.6001E+04 while B form changes from -2.4745E+04
to -3.8989E+04 in a water box.
First, does it mean it has a B form DNA starting structure with
somewhat higher energy? and the first minimized B form structure is
less stable than A from mininized structure?

My question is about how we can mention the stability of the molecule
in terms of energy in this case.
Same comparison can go on with tutorial's data.
Minimization2: (B) -3.9276 -> -4.1777E+04
                             (A) -4.6577 -> -4.9411E+04
heating Dynamincs (B) -44677.2451 -> -32447.7077
                                     (A) -52921.4514 -> -37836.6256
Dynamics2 (B) -32534.5748 -> -33533.4505
                       (A) -38138 -> -39319

What I understood is in considering A, the starting energy is getting
lower while it changed into B form DNA. Anyway, my ultimate question is
if there is a way that we can simply compare stability/ energy of
current conformation of the molecule.

with big thanks in advance,

Young Jin

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