From: Peter Freddolino (petefred_at_umich.edu)
Date: Mon Nov 30 2020 - 19:28:16 CST
Hi Francesco,
NAMDenergy is going to give you the interaction energy that the force field
gives you; no more, and no less. The pairwise additive force fields that
we're typically talking about here don't have any more complex hydrogen
bonding terms , and in particular don't take hydrogen bonding angles into
account (this is a well known aspect of the approximations made by these
force fields). If you want to, you could instead extract the distances and
angles from the trajectory using a tcl script and either analyze them
directly, or look at them in the context of some more complex functional
form for hydrogen bonding energies.
Best,
Peter
On Mon, Nov 30, 2020 at 1:02 PM Francesco Pietra <chiendarret_at_gmail.com>
wrote:
> Hello
> 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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