On Tue, Jul 07, 2026, Jessica Baa via AMBER wrote:
>
>While trying to compute the binding free energy of a protein complex (2700
>amino acids) with another protein (550 amino acids), I am getting highly
>positive delta G (~10^16 kcal/mol)
>
>Is MMPBSA tool in AMBER capable of revealing the protein-protein binding
>free energy for large complexes. If so, k let me know what might be
>possibly wrong with my inputs.
You need to look at the individual mdout files for clues about what went
wrong. With an absurd answer (like 10^16 kcal), see if there is one outlier
energy, or are all individual snapshots giving obviously wrong energies? Is
there some component of the energies that stands out? etc.
...good luck....dac
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Received on Sat Jul 11 2026 - 07:30:03 PDT
