[gmx-users] deltaG is positive after FEP

[Dries Van Rompaey]

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" <scinikhil at 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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