AMBER Archive (2003)

Subject: energy calculation

From: thenmalar rathinavelan (thenmalrr_at_yahoo.co.in)
Date: Sun Feb 09 2003 - 01:19:59 CST

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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