AMBER Archive (2000)

Subject: MM_GBSA and DNA methylation

From: Sylvie Derreumaux (derreuma_at_igr.fr)
Date: Wed Oct 25 2000 - 09:06:17 CDT

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