Hi,
So far you have only completed one part of the simulation. You have to
close the thermodynamic cycle in order to be able to calculate what the
effect of the mutation is in your protein. Take a look at alchemistry.org
for tutorials and relevant information on this topic.
On 01 Sep 2017 7:20 AM, "Nikhil Maroli" <scinik...@gmail.com> wrote:
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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