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
