ff19sb should not be used with TIP3P, as noted in the ff19sb article, the
amber web site and the amber manual.
On Wed, May 6, 2026, 2:39 AM Surabhi Singh 24933024 via AMBER <
amber.ambermd.org> wrote:
> Hello Amber Team,
>
> I am working on a protein–DNA complex (bHLH transcription factor). During
> the production run, I observe that the longer helical region becomes highly
> flexible and shows noticeable bending near the center.
>
> Protocol followed:
>
> 1. Forcefield used : Amber: ff19SB, OL24, TIP3P water model
> 2. Salt conc: 150mM Nacl
> 3. Energy minimization
> 4. Three equilibration stages (~1.15 ns total, first two with restrain
> and last one without restrain)
> 5. Production MD: 250 ns (trajectory appears stable overall)
>
>
> The total and potential energies remain stable with no significant
> deviations, yet the helix undergoes bending.
>
> Question:
> 1. How should this bending be interpreted despite stable energy profiles?
> Is this expected behavior (e.g., intrinsic flexibility), or could it
> indicate an issue with the setup?
>
> Thank you for your guidance.
>
> Thanks and Regards
> Surabhi Singh
> Ph.D. Computational Biology
> Biosciences and Bioengineering, IIT Roorkee
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Received on Wed May 06 2026 - 04:30:04 PDT
