Re: energy calculation

From: Carlos Simmerling <>
Date: Sun 9 Feb 2003 08:27:03 -0500

It isn't completely clear to me what energies you are
comparing. You said the two systems have a different
# of waters, but are they different sequences or different
base pair geometries for the same sequence?
You can only really compare different conformations
for the same sequence. Otherwise the zero of energy
is not the same. If they are the same sequence, I'd suggest
using an MM-PBSA analysis of the snapshots after removing
the water, since you certainly need to include solvent effects
but you can't have a different amount of solvent (and the
explicit solvent energies are also noisy, etc.)
Carlos L. Simmerling, Ph.D.
Assistant Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web:
Stony Brook, NY 11794-5115 E-mail:

----- Original Message -----
From: "thenmalar rathinavelan" <>
To: <>
Sent: Sunday, February 09, 2003 2:19 AM
Subject: energy calculation

> Dear ambers,
> I want to compare the energies of two DNA systems
> for which I have done a few nanoseconds dynamics
> (same
> input parameters used for dynamics). Among these two
> DNA systems one of them comprises a mismatch. When I
> compare the energies (DNA alone), the energy of the
> DNA system with mismach is lower (90 kcal/mol) than
> the energy of the DNA system with perfect Watson&
> Crick base pair (!!). Moreover, the differnce in
> energy mainly arises due to non-bonded electrostatic
> energy term. If the energies of the whole system is
> considered, i.e. with water&ion, also gives similar
> trend in energy. It is to be mentioned here that the
> mismatch system has more number of water molecules
> (around 100) than the perfect W&C system.
> I like to know what is wrong in the calculation or
> what would be the reason for this. Kindly, point out
> my mistake or tell your suggestions regarding this.
> Thank you very much in advance.
> Thenmalar
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Received on Sun Feb 09 2003 - 05:27:03 PST
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