ff19sb should not be used with TIP3P water.
On Tue, May 12, 2026, 12:56 AM Surabhi Singh 24933024 via AMBER <
amber.ambermd.org> wrote:
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> So, the force fields I am using are ff19SB, OL24 and TIP3P.
> I have attached the file ( input and results are there).
>
>
> Thanks and Regards
> Surabhi Singh
> Ph.D. Computational Biology
> Biosciences and Bioengineering, IIT Roorkee
>
>
> On Tue, May 12, 2026 at 2:06 AM Ray Luo <rluo.uci.edu> wrote:
>
> > Maybe it's a good idea to share your detailed MMPBSA energy report for us
> > to see what's going on.
> >
> > Ray
> > --
> > Ray Luo, Ph.D.
> > Professor of Structural Biology/Biochemistry/Biophysics,
> > Chemical, Applied and Materials Physics,
> > Chemical and Biomolecular Engineering,
> > Materials Science and Engineering, and
> > Biomedical Engineering
> > Department of Molecular Biology and Biochemistry
> > University of California, Irvine, CA 92697-3900
> >
> >
> > On Mon, May 11, 2026 at 6:04 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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> >>
> >>
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> >>
> >
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Received on Tue May 12 2026 - 05:00:02 PDT
