see the reply from Jiri Sponer - do you have good experimental data that
the helices are not bent?
On Fri, May 15, 2026 at 12:54 AM Surabhi Singh 24933024 <
surabhi_s.bt.iitr.ac.in> wrote:
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> Hey Carlos,
>
> I understand. However, even when using the more updated setup with ff19SB,
> OPC water, and OL24, I still observe bending in the helical region of the
> protein during the simulation.
> Interestingly, when I run the same system using ff14SB, OL15, and TIP3P,
> the helical region remains stable and I do not observe this bending
> behavior.
> Since ff19SB + OL24 + OPC is generally considered a more refined and
> accurate combination according to recent literature, I am trying to
> understand why this issue is occurring in my case and whether I may be
> missing something in the simulation setup or equilibration protocol.
>
> At this point, I am considering continuing with ff14SB + OL15 + TIP3P
> because the structure appears more stable there, although I understand it
> may not represent the most updated parameter combination.
>
>
> Thanks,
> Surabhi Singh
>
>
>
> On Wed, May 6, 2026 at 4:32 PM Carlos Simmerling <
> carlos.simmerling.stonybrook.edu> wrote:
>
>> 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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>>> AMBER.ambermd.org
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>>
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Received on Fri May 15 2026 - 07:00:03 PDT
