Dear Amber Users!
At present moment, I am dealing with the modeling of the enzymes from
xylanase subfamily, which have several flexible loops of crusial
functional importance in shielding of the active site and thus in
being significative for tayloring of the enzyme to its substrate.
Could you tell me which thermostat that had been emplemented in Amber
should be better option to reproduse dynamics of such inherently
dynamical systems (with flexible loops) assuming that I model it with
complex with substrate (sugar, parametrized by GLYCAM) as well as in
the apo-state?
Notably, actually I have tried to use Berendsen method, which probably
was not good solution for the modeling in nanosecond range.
# equilibrate
ntt=1, tempi=0.5, temp0=310.0,
#run production
ntt=1, tempi=0.1, temp0=310.0,
May the switching to Langeving dynamics in the following manner be
better for the modeling of such system?
#run equilibration
ntt=3, temp0=310, gamma_ln=5
#run production
ntt=3, temp0=310, gamma_ln=1
Yours with thanks,
Prof. James Starlight Jr.
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Received on Tue Jun 25 2019 - 11:30:02 PDT
