Hello,
This is a question regarding the electrostatic term of the DNA internal
energy calculated by anal with MM_GBSA (no cutoff and epsilon=1).
I have performed energy calculations and compared the results for two
related DNA 16mers: the DNAs have the same sequence but one of them has two
5-methylated cytosines. Results are averaged values for 10000 snapshots from
10ns MD.
I don't understand why the DNA electrostatic internal energy is about 150
kcal/mol higher for the methylated oligonucleotide, whereas the two averaged
structures are very closed (rmsd < 0.3 A) and the methyl groups are nonpolar.
Thank you for your help.
Sylvie
Sylvie Derreumaux
CNRS UMR 8532
Institut Gustave Roussy, PR2
39 rue Camille Desmoulins
94805 Villejuif cedex
France
Received on Wed Oct 25 2000 - 07:06:17 PDT
