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UCL-CCS / TIES

Topology Superimposition based on joint graph traversal
MIT License
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Further investigation into zero-sum with L6 #181

Closed bieniekmateusz closed 2 years ago

bieniekmateusz commented 4 years ago

this is where the cl-br mutation takes place, with 2 atoms it gives very strange energies, but here it is perfect

-------------------------   lig    ----------------------
                  Elec         vdW       Subtotal
---------------------------------------------------------
Part 1(app)      2.7247  |   0.1250  |  2.8497     
Part 2(disapp)   2.7257   |   0.1275  |  2.8532
---------------------------------------------------------
Subtotal        -0.0010  |  -0.0025  | -0.0035
---------------------------------------------------------
-bash-4.2$ pwd
/lustre/scafellpike/local/HT03119/mjm06/mxb57-mjm06/odd_ptp1b/left2/case_c12c38
bieniekmateusz commented 4 years ago

Interestingly, when one of the ester atoms is being modified, there is a slight elec and vdw difference, would this happen again? the difference was much more striking in the ptp1b l6-l14 case when the same ester oxygen was being mutated

-bash-4.2$ cat ./case_o37o43/ddg.out

-------------------------   lig    ----------------------
                  Elec         vdW       Subtotal
---------------------------------------------------------
Part 1(app)     -53.9824  |   6.7096  | -47.2729     
Part 2(disapp)  -54.0836   |   6.8294  | -47.2542
---------------------------------------------------------
Subtotal         0.1012  |  -0.1198  | -0.0187
---------------------------------------------------------

Edit: another attempt at this shows that there is a clear pattern to this mutation skewing numbers. Although the changes cancel each other out. 

                  Elec         vdW       Subtotal
---------------------------------------------------------
Part 1(app)     -54.3392  |   6.9805  | -47.3587     
Part 2(disapp)  -54.1525   |   6.8029  | -47.3496
---------------------------------------------------------
Subtotal        -0.1867  |   0.1776  | -0.0091
bieniekmateusz commented 4 years ago

Out of all these cases it is only 1 that is non-zero, cases: ./case_c7c59/ddg.out ./case_cl8cl9/ddg.out ./case_c24c46/ddg.out ./case_c27c49/ddg.out ./case_o37o43/ddg.out ./case_s33s35/ddg.out ./case_c12c38/ddg.out

bieniekmateusz commented 4 years ago

It appears that O37 is one of the more charged cases (-0.82), whereas the next is C12 with -0.12. Let's try several other charged residues. Candidates: C2 : 0.89 C23 : -0.24 C35: 0.93 H43 : 0.38 N15 -0.70 N19 -0.82 Other Os S20 : 1.44 Let's just try

bieniekmateusz commented 4 years ago

So the new cases are: case_s20s34 case_o37o36o42o43 case_o36o42 case_n19n21 case_h43h66 case_c35c56 case_c2c44

bieniekmateusz commented 4 years ago

In s20s34 we are removing a slightly larger chunk: with both S and the attach oxygens and the ring that was previously done, this leads to a small discrepancy. Is the S cancelling out with Os? 

-------------------------   lig    ----------------------
                  Elec         vdW       Subtotal
---------------------------------------------------------
Part 1(app)     -72.8944  |   6.2798  | -66.6146     
Part 2(disapp)  -72.9504   |   6.4177  | -66.5328
---------------------------------------------------------
Subtotal         0.0560  |  -0.1378  | -0.0818
---------------------------------------------------------
bieniekmateusz commented 4 years ago

Removing the other oxygen from the same carboxylic group did not give exactly the same results, being much closer to 0:

                  Elec         vdW       Subtotal
---------------------------------------------------------
Part 1(app)     -56.1556  |   5.7701  | -50.3855     
Part 2(disapp)  -56.2134   |   5.8194  | -50.3940
---------------------------------------------------------
Subtotal         0.0578  |  -0.0493  |  0.0085

is it just sampling? most likely

bieniekmateusz commented 4 years ago

the relatively highly charged standalone H43h66 mutation also goes back very well to 0:

-------------------------   lig    ----------------------
                  Elec         vdW       Subtotal
---------------------------------------------------------
Part 1(app)     24.5498  |  -0.1399  | 24.4100     
Part 2(disapp)  24.5464   |  -0.1392  | 24.4073
---------------------------------------------------------
Subtotal         0.0034  |  -0.0007  |  0.0027
---------------------------------------------------------
bieniekmateusz commented 4 years ago

Removing both oxygen in the carboxylic group together is fine as well:

                  Elec         vdW       Subtotal
---------------------------------------------------------
Part 1(app)     -14.1054  |  11.4595  | -2.6459     
Part 2(disapp)  -14.0820   |  11.4298  | -2.6523
---------------------------------------------------------
Subtotal        -0.0233  |   0.0297  |  0.0064

This extended with removing the entire carboxylic group with the extra c35 is also fine

                  Elec         vdW       Subtotal
---------------------------------------------------------
Part 1(app)     -88.0457  |  20.3691  | -67.6765     
Part 2(disapp)  -88.0007   |  20.3189  | -67.6818
---------------------------------------------------------
Subtotal        -0.0449  |   0.0502  |  0.0053
bieniekmateusz commented 4 years ago

Removing a slightly larger chunk with N creates some errors

                  Elec         vdW       Subtotal
---------------------------------------------------------
Part 1(app)     -63.4380  |   2.4582  | -60.9798     
Part 2(disapp)  -63.5950   |   2.4211  | -61.1739
---------------------------------------------------------
Subtotal         0.1570  |   0.0370  |  0.1941

it should be similar to the S20 case. No vdw problems but electrostatics increases only slightly. Nothing close to explaining the main case.

bieniekmateusz commented 4 years ago

Removing the carboxylic group on the other molecule is also fine (c2c44)

                  Elec         vdW       Subtotal
---------------------------------------------------------
Part 1(app)     -82.1433  |  22.5391  | -59.6043     
Part 2(disapp)  -82.2372   |  22.5559  | -59.6813
---------------------------------------------------------
Subtotal         0.0938  |  -0.0168  |  0.0770
bieniekmateusz commented 4 years ago

we see the same distribution and dependance, but the energies here have no problems, so this is not the issue at all l6l6_sameDist

bieniekmateusz commented 4 years ago

Should it not be oscillating around 0 ring_c_dst