Dear all,
I did a transformation of aa H->A using hybrid topology and performed FEP
calculations. At the end im getting the positive value of DG (47.99 +/-
0.56).
1. it depicts that the mutation of H->A is not favourable to the
protein? I have provided a link to the Free energy differences plot.
2. Should I try A->H transformation/Reverse transformation?
delta lamda =0.5, 10 ns simulation and histogram looks fine.
Here are the output details.
Temperature: 300 K
Detailed results in kT (see help for explanation):
lam_A lam_B DG +/- s_A +/- s_B +/- stdev +/-
0 1 4.38 0.18 1.61 0.10 1.96 0.17 1.90 0.07
1 2 1.71 0.12 0.93 0.07 1.13 0.10 1.39 0.05
2 3 0.96 0.05 0.32 0.04 0.37 0.04 0.93 0.02
3 4 0.98 0.05 0.22 0.03 0.26 0.03 0.79 0.01
4 5 1.00 0.04 0.20 0.03 0.23 0.03 0.70 0.01
5 6 0.94 0.03 0.25 0.03 0.28 0.02 0.65 0.01
6 7 0.92 0.03 0.16 0.03 0.18 0.03 0.60 0.01
7 8 0.94 0.01 0.16 0.04 0.19 0.04 0.58 0.01
8 9 0.99 0.02 0.12 0.02 0.14 0.02 0.56 0.00
9 10 0.90 0.02 0.25 0.03 0.28 0.03 0.62 0.01
10 11 0.80 0.02 0.18 0.04 0.23 0.04 0.67 0.02
11 12 0.74 0.04 0.23 0.07 0.26 0.08 0.69 0.03
12 13 0.66 0.05 0.19 0.05 0.23 0.06 0.67 0.02
13 14 0.57 0.02 0.25 0.02 0.26 0.02 0.65 0.02
14 15 0.65 0.02 0.10 0.02 0.11 0.02 0.57 0.01
15 16 0.62 0.02 0.29 0.03 0.30 0.03 0.62 0.01
16 17 0.62 0.02 0.12 0.03 0.13 0.03 0.59 0.01
17 18 0.54 0.01 0.31 0.01 0.34 0.01 0.71 0.00
18 19 0.19 0.05 0.43 0.04 0.47 0.04 0.90 0.01
19 20 0.13 0.04 0.20 0.07 0.13 0.04 0.68 0.02
Final results in kJ/mol:
point 0 - 1, DG 10.92 +/- 0.45
point 1 - 2, DG 4.26 +/- 0.31
point 2 - 3, DG 2.40 +/- 0.12
point 3 - 4, DG 2.45 +/- 0.11
point 4 - 5, DG 2.51 +/- 0.11
point 5 - 6, DG 2.34 +/- 0.06
point 6 - 7, DG 2.31 +/- 0.08
point 7 - 8, DG 2.35 +/- 0.01
point 8 - 9, DG 2.47 +/- 0.05
point 9 - 10, DG 2.25 +/- 0.06
point 10 - 11, DG 1.99 +/- 0.05
point 11 - 12, DG 1.84 +/- 0.11
point 12 - 13, DG 1.64 +/- 0.12
point 13 - 14, DG 1.42 +/- 0.05
point 14 - 15, DG 1.61 +/- 0.05
point 15 - 16, DG 1.54 +/- 0.06
point 16 - 17, DG 1.56 +/- 0.06
point 17 - 18, DG 1.34 +/- 0.04
point 18 - 19, DG 0.47 +/- 0.13
point 19 - 20, DG 0.33 +/- 0.11
total 0 - 20, DG 47.99 +/- 0.56
https://drive.google.com/file/d/0BxaQk_pcR9viUmYwbUItajltNXM/view?
usp=sharing
Thanks
--
Regards,
Nikhil Maroli
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