Hi,
I am trying ABFE in amber24 with restraints on disappearing ligand. I
found here on mailing list that default lambda-sheduling is intended for
RBFE, particularly restraints on disappearing softcore atoms are turned
off at lambda 1 and one can change this behavior by setting "TypeRestBA,
linear, symmetric, 1.0, 1.1" in lambda.sch file.
In amber24 manual you claim that default setting correspond to
lambda.sch file:
TypeGen, linear, complementary, 0.0, 1.0
TypeBAT, linear, symmetric, 0.0, 1.0
TypeEleRec, linear, symmetric, 0.0, 1.0
TypeEleCC, smooth_step2, symmetric, 0.0, 1.0
TypeEleSC, smooth_step2, symmetric, 0.0, 1.0
TypeVDW, smooth_step2, symmetric, 0.0, 1.0
BTW there is mistake in manual with additional spaces in "smooth_ step2"
in last two lines, which does not cause error, but my simulations
crashed at lambda = 0.
Mistake in manual:
TypeEleSC, smooth_ step2, symmetric, 0.0, 1.0
TypeVDW, smooth_ step2, symmetric, 0.0, 1.0
I noticed that having lambda.sch file with above "default" parameters in
working directory significantly changes energies, with quite high energy
difference at endpoins, which can be seen for example in remlog file
from hamiltonian replica exchange.
without lambda.sch file:
# exchange 100
1 2 300.00-208725.86-208417.26 -Infinity 0.11 T
0.56
2 1 300.00-208416.79-208725.37 -0.08 -0.30 T
0.44
3 4 300.00-208787.25-208647.18 0.31 -0.25 T
0.60
4 3 300.00-208646.48-208787.33 0.38 -0.51 T
0.56
5 6 300.00-208665.78-208174.26 0.51 -0.64 T
0.60
6 5 300.00-208173.70-208665.42 0.53 -0.58 T
0.56
7 8 300.00-208626.48-208474.09 0.51 -0.44 T
0.66
8 7 300.00-208473.42-208625.93 0.41 -0.56 T
0.56
9 10 300.00-208190.57-207976.46 0.52 -0.46 F
0.70
10 9 300.00-207976.97-208189.78 0.48 -0.53 F
0.74
11 12 300.00-208751.70-208939.23 0.63 -0.59 T
0.54
12 11 300.00-208938.46-208751.10 0.58 -0.56 T
0.64
13 14 300.00-208480.67-207801.76 0.53 -0.38 F
0.48
14 13 300.00-207801.92-208480.29 0.37 -0.35 F
0.56
15 16 300.00-208635.54-208381.70 0.35 -0.15 T
0.54
16 15 300.00-208381.36-208635.51 -0.29 0.00 T
0.00
with lambda.sch file:
# exchange 100
1 2 300.00-208637.45-208802.00 -Infinity -11.97 T
0.50
2 1 300.00-208789.68-208624.92 12.11 -0.29 T
0.34
3 4 300.00-208159.57-208099.11 0.10 1.16 T
0.52
4 3 300.00-208100.17-208160.69 -1.08 1.92 T
0.58
5 6 300.00-208369.50-208261.84 -1.81 2.10 F
0.62
6 5 300.00-208264.58-208370.91 -1.93 1.91 F
0.66
7 8 300.00-208550.45-208430.67 -1.93 1.65 T
0.62
8 7 300.00-208432.59-208552.29 -1.80 1.76 T
0.64
9 10 300.00-208621.16-208270.66 -1.71 1.68 F
0.68
10 9 300.00-208273.01-208622.81 -1.69 1.91 F
0.70
11 12 300.00-208313.97-208668.38 -1.83 1.89 T
0.74
12 11 300.00-208669.94-208316.07 -1.93 1.78 T
0.76
13 14 300.00-208527.67-208193.53 -1.80 1.07 F
0.66
14 13 300.00-208194.47-208528.42 -1.02 -0.46 F
0.48
15 16 300.00-208488.22-208502.42 0.40 -12.23 F
0.48
16 15 300.00-208490.40-208475.60 11.73 0.00 F
0.00
This suggest, that default settings in amber24 are different than
settings claimed in manual.
Can somebody provide correct default settings?
thanks,
Juraj Dobias
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Received on Thu May 23 2024 - 00:30:02 PDT
