Dear AMBER users,
I performed per-residue decomposition analysis using python script in
AMBER11. A hydrogen bond between sulfonamide nitrogen (acceptor) of
inhibitor and carboxylic oxygen (donor) of aspartic acid residue was
consistent throughout the simulation of 25 ns (Average distance 2.82
angstrom). However, higher value was observed for polar solvation term than
the electrostatic contribution term which led hydrogen bond as unfavorable
interactions. Following are the details of calculation.
*Residue*
*Glu*
*VDW*
*-1.66*
*ESURF*
*-0.21*
*VDWTOT*
*-1.87*
*EEL*
*-10.22*
*EGB*
*11.84*
*ELETOT*
*1.62*
*GBTOT*
*-0.25*
So does the calculation is right and consistent hydrogen bond is
unfavorable interaction? Or the polar contribution is overestimated in the
MM-GBSA calculation?
Thanks and regards,
Ranajit Shinde
Ph.D. scholar,
NIPER, Mohali, India
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Received on Sat Dec 15 2012 - 04:30:02 PST
