Dear all,
I ran an MD simulation of a protein which has one non-standard amino-acid.
I used MMPBSA.py to calculate the binding free energy (with pairwise
residue decomposition). There were two observations that I did not
understand:
1. What does the pairwise decomposition of a residue with itself mean? For
example, what does the energy decomposition between Ser1 and Ser1 pair mean?
2. The backbones of the non-standard amino acid had zero energy
contribution. All the energy was that of the sidechain interactions. Why is
that so?
I would really appreciate your help and comments on this!
Thank you!
Kindest regards,
Sara I Omar
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Received on Mon Oct 05 2015 - 22:30:04 PDT
