RE: energy calculation

From: Yong Duan <>
Date: Sun 9 Feb 2003 11:36:28 -0500

Dear Thenmalar:

My guess is this is due to the difference in the number of water
molecules which overwhelmed the small energy difference due to the
mismatch (which is on the order of kcal per hydrogen bond). The energy
of "solvation" of water is also on the order of kcal and is negative
(water likes to stay with other water molecules) but you have about 100
more water molecules in the mismatched system. It's mainly

You can use the intra-molecular energies to get the difference. This
assumes that your mismatched DNA still retains the base-pairing at the
mismatch. If, on the other hand, one of the bases are exposed to
solvent, you probably need to consider the solvation effect which is
probably a little difficult for your present setup.


-----Original Message-----
From: thenmalar rathinavelan []
Sent: Sunday, February 09, 2003 2:20 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
 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.

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Received on Sun Feb 09 2003 - 08:36:28 PST
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