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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Received on Thu May 14 2026 - 22:00:02 PDT
