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 Mon Oct 06 2025 - 04:00:02 PDT
