Dear users,
Are the energy terms given in amber .out file and those calculated by
MMPBSA analysis equivalent?
As far as i understand, .out file energies are composed of potential and
kinetic energy terms. We usually take a cut off of 10 Ang for all non
bonded interactions. So does .out energies contains solvation energy and
entropy component as well or is it just the MM energies?
My doubt arose because if one wants to do stability calculations in case of
single RNA species and its single point mutants trajectories, what should
be the correct approach?
Furthermore, i had some Mg2+ ions in the original crystal structure, and 2
of them directly contact RNA backbone. Should i treat these ions as ligands
, in case of MMPBSA or it is better to remove them?
Thank you,
Asmi
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Received on Thu Jun 27 2013 - 23:30:02 PDT
