[AMBER] high positive values for VDW interactions using LIE function

From: Pirhadi, Somayeh via AMBER <amber.ambermd.org>
Date: Wed, 13 Sep 2023 18:09:58 +0000

Hi Everyone,

In my study, I used the Linear Interaction Energy (LIE) function to calculate van der Waals (VDW) and electrostatic interaction energies for all pairwise residues in a simulation trajectory based on the 6DGX PDB code. However, I have noticed that I am obtaining notably high positive values for the VDW energies when analyzing interactions between residues connected through a peptide bond. Is the Ok to have such positive large values?
Here's an example of the cpptraj command I employed:

cpptraj
parm comp.prmtop
trajin 11md.dcd
lie l :197 :198 out e197-e198.txt
run
quit

Below is the header of the resulting e197-e198.txt file:

#Frame l[EELEC] l[EVDW]
       1 -29.5847 30438.4070
       2 -26.0282 22174.7352
       3 -30.0953 23456.4045
       4 -25.9953 34334.1054
       5 -28.7155 29136.5942
       6 -31.9867 20931.3849
       7 -31.8298 26044.2456
       8 -26.9731 27504.0629
       9 -25.3862 21537.3716

I would greatly appreciate any insights or advice you might have regarding these high positive VDW energy values.

Thank you,
Best regard,
Somayeh Pirhadi, Postdoc
UMass Chan Medical School

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Received on Wed Sep 13 2023 - 11:30:02 PDT
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