[gmx-users] deltaG is positive after FEP

[Nikhil Maroli]

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