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 - 06:00:02 PDT
