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 Sat Feb 08 2003 - 23:19:59 PST
