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-- 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 > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > > https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!CzAuKJ42GuquVTTmVmPViYEvSg!Oxa8Orpw4rbuJT9soZl03JYiFpkQ0RYVXKnJE_Bcg5_ArjwHfbNw0mBGGzBRih-mj8VS3thvGFU$ > _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Mon May 11 2026 - 14:00:02 PDT