Hello Amber Team,
I am currently working on *protein–DNA complexes *and have completed energy
minimization followed by 250 ns production MD simulations.
I am now performing MMPBSA calculations for multiple complexes involving
protein bound to standard DNA as well as mutated DNA sequences. In my
setup, I considered the protein as the receptor and DNA as the ligand.
However, I am observing positive ΔG binding values for these systems, which
is confusing because, for other complexes analyzed using the same workflow
and parameters, I obtained negative ΔG values as expected.
I would like to understand the possible reasons behind these positive
binding free energies. Could this be related to the highly charged nature
of protein–DNA systems and electrostatic contributions affecting the MMPBSA
calculations? Or is there something specific that should be considered
while applying MMPBSA to protein–DNA complexes?
I would greatly appreciate any suggestions or insights regarding this issue.
Thanks,
Surabhi Singh
Ph.D. Computational Biology
Biosciences and Bioengineering, IIT Roorkee
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Received on Mon May 11 2026 - 06:30:02 PDT
