Hey there!
What version of amber are you using?
Best,
Kevin
> On May 11, 2026, at 9:04 AM, Surabhi Singh 24933024 via AMBER <amber.ambermd.org> wrote:
>
> 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 - 07:30:02 PDT
