NamdEnergy Nonbonded H-bonds

From: Francesco Pietra (
Date: Mon Nov 30 2020 - 11:06:52 CST

I am aware of the series of posts by Madhavi-Fiorin-Freddolino about
NamdEnergy and Nonbonded.
Related to that, I would like to make known what I am observing with a
protein and its peptide ligand where, according to X-ray diffraction from
the crystal at very low temperature, several possible H-bonds may be
involved in stabilizing the receptor-ligand complex.

I carried out a series DFT QMMM (PBE0 D3BJ def2-SVP level) in explicit
water at 310K for the atoms presumably involved in these H-bonds. All
crystal water was retained in MD and included in QMMM when involved. Then,
the QMMM-only psf/dcd was analyzed by implicit solvent NamdEnergy with
default cutoff and dielectric according to the values suggested by Li et al
JCTC 2013 for the residues involved (around 20).

I find the resulting Nonbonded Energy values (highest -3.5, lowest -0.3
kcal/mol) mostly unrelated to what is expected from H-bonds on visualizing
the trajectory (I mean H-O or H-N distances and related angles). My
question is whether there is a way to tune the NamdEnergy plugin better in
order to emphasize the role of H-bonding.

Thanks for advice
francesco pietra

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