Hi,
The manual is your friend here. The 'lie' command by default uses a
cutoff for non-bonded interactions:
"Electrostatic and van der Waals interactions will be calculated for
all atom pairs. A separate electrostatic and van der Waals cuto can
be applied, the default is 12.0 Angstroms for both."
The "simple" non-bonded energy model used by the 'energy' command by
default has no cutoff:
"Note that the non-bonded energy terms for 'simple' do not take into
account periodicity and there is no distance cut-o ff. "
I suspect this is where the discrepancy lies.
-Dan
On Tue, Jun 24, 2025 at 8:35 AM Игорь Упоров via AMBER
<amber.ambermd.org> wrote:
>
> Dear AMBER users,
> I work with complexes=protein + ligand (like 3PB9, 6GBX structures).
> Analysing results I've noticed disagreement in calculations of nonbond
> energies using cpptraj "energy" and "lie" commands. According to the
> manual both commands - "Electrostatic and van der Waals interactions will
> be calculated for all atom pairs". However, the results are different.
> First, I "rms first :1-330", strip solvent and saved trajectory in .nc
> format.
>
> Then to calculate interaction energy between protein and ligand I used:
>
> lie :330 :1-329 out Enbond.csv
>
> FOr fist frame:
>
> Eelec EVDW Total
> -69.8609 -30.4499 -100,3108
>
> Then I've decided to calculate nonbond energy in a different way.
> Command :
>
> energy :1-330 out Etotal.csv
>
> decomposes total potential energy of the system by bond streching,bond
> deformation..., VdW, Electrostatic written in columns. Again, the manual
> states that on default all pairs of atoms included in calculation for whole
> system. So, if I calculate
>
> EVDW(complex)-EVDW(protein)-EVDW(ligand) and same for Eelec
>
> All contributions from pairs of atoms belonging to the same particular
> system (complex, protein, ligand) get cancelled out, and only pairs of
> atoms one from protein and one from ligand left. Am I right? Interaction
> energy calculated by this method for 1st frame
>
> Eelec EVDW Total
> -151.7 -35.7 -187.4
>
> Such a difference can be seen for trajectory frames.
> Could you please explain to me the reason for such difference. Am I missing
> something?
>
> Thank you.
> UIV.
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Received on Tue Jun 24 2025 - 06:30:01 PDT
