Hi everyone,
I am trying to calculate pairwise non-bonded interaction energy for a protein. I have tried two methods.
First I try the MM/GBSA method and the idecomp was set to 4 and dec_verbose was set to 1. However, in the output file in the Total Energy Decomposition part, the TOTAL interaction energy (comprisng all 5 terms) between Res1 and Res1 (itself) is -22 kcal/mol. I think it's strange since there should not be any interaction energy between one residue.
Then I trid the seconde method, pairwise in CPPTRAJ. Using this method, I might realise why the interaction energy between one residue is non-zero (because they are calculated at atomic level). However, taking Res1 as example, the sum of Eele and Evdw for Res1-Res1 is -35.3044 kcal/mol while MM/GBSA gave 40.5 kcal/mol (only van der Waals and electrostatics terms were summerized).
These results confused me since the two method gave inconsistent results. I wonder that which is the "standard" method for calculating pairwise non-bonded interaction energy and why these two methods gave different results.
Also, I found that it seems not easy to obtain residue level pairwise interaction energy by "pairwise". Is there any tricks to easily convert the atom-level pairwise interaction energy to residue level?
Looking forward to the replys and thanks a lot.
All the best,
Chanyan
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Received on Tue May 09 2023 - 06:30:03 PDT
