On Sat, 2015-04-11 at 12:35 +0800, windy wrote:
> Thanks for you reply ,
>
> I'd like to show some sentences in that paper:
>
> " To examine the free energy of the covalent-orlistat ligand in each
> hexyl tail conformation, a total of 50 snapshots over the course of
> each conformation in each simulation were extracted from the
> simulation trajectories of FASN TE."
> " The free energy was calculated and decomposed to
> covalent-orlistat residue using the MM_PBSA module of AMBER by the
> equation PB_tot=PB_sol+ gas, where PB_sol= PB_sur +PB_cal and gas =
> ELE + VDW + INT. PB_sur is described as the hydrophobic contributions
> to solvation free energy for PB calculations, and PB_cal is described
> as the reaction field energy calculated by PB. ELE is the nonbonded
> electrostatic energy +1,4-electrostatic energy; VDW is the nonbonded
> van der Waals energy +1,4-van der Waals energy; and INT is the bond,
> angle, and dihedral energies. Additionally, to demonstrate that the
> two conformations of covalent-orlistat are independent, distinct, and
> not a result of the influence from the protein, two 100 ns
> trajectories were run for the 3-mer peptide, which is composed of
> covalent-orlistat bonded to Serflanked by two Gly residues, and the
> free energy decomposed to covalent-orlistat was evaluated with a total
> of 50 snapshots in each conformation using the MM_PBSA module. "
It's important to note that what they are describing here is *not* a
binding free energy calculation, but rather a so-called "stability"
calculation (where they compute single-point energies of different
conformations to compare their relative stabilities). This is, of
course, perfectly fine to use with MM/PBSA methodologies, but it could
not have been used to compute a binding free energy for the covalent
complex.
>
> How the decomposation achieve? Maybe the key point rely on the INT ,it
> is the bond, angle and dihedral energies and not occur often in
> regular MM_PBSA method.
Look at the &decomp namelist variables section in the MMPBSA.py chapter
of the Amber 14 manual (page 575).
>
> I am also try QM/MM method , but I want to know whether the two
> methods is consistent.
I do not think QM/MM is compatible with decomposition analysis.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Apr 14 2015 - 08:00:04 PDT
