Hi,
If you're having issues with system relaxation, you may want to try this script:
https://github.com/drroe/AmberMdPrep
Which implements the explicit solvent relaxation protocol detailed in
this publication: https://doi.org/10.1063/5.0013849
Good luck,
-Dan
On Mon, Oct 6, 2025 at 6:41 AM Patil Pranita Uttamrao via AMBER
<amber.ambermd.org> wrote:
>
> Dear AMBER developers and users,
>
> I am currently facing an issue during the minimization step of my system
> with multiple chains in AMBER, which looks fine after system preparation
> using tleap without any error. The water box appears to be breaking apart,
> and I observe the formation of holes in the solvent box and after few steps
> the protein system is then moving out of the waterbox during equilibration
> itself. I am using *AMBER 16 with ff14SB forcefield using TIP3P water
> model.*
>
> *Below is the step1 minimization input file.*
>
> Protein
> &cntrl
> imin = 1,
> maxcyc = 1000,
> ncyc = 500,
> ntb = 1,
> ntr = 1,
> cut = 10.0
> /
> Hold the PROTEIN fixed
> 500.0
> RES 1 397
> END
> END
>
> Could anyone please suggest what might be causing this issue or how to
> avoid the water box distortion during minimization?
>
> --
>
>
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Received on Tue Oct 07 2025 - 08:30:02 PDT
