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sofia's_edits #2

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9a67402
Add files via upload
djcole56 Jul 13, 2020
411e730
Update README.md
CRingrose94 Jul 14, 2020
b62a420
Update README.md
CRingrose94 Jul 14, 2020
3cd2900
Create fragment_energetics.py
CRingrose94 Jul 14, 2020
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Create protein_energetics.py
CRingrose94 Jul 14, 2020
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lefnelso Jul 16, 2020
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lefnelso Jul 16, 2020
b43a4ea
Delete Lig1.pdb
lefnelso Jul 16, 2020
7926330
Delete Lig1.xml
lefnelso Jul 16, 2020
202d9ca
Delete Lig10.pdb
lefnelso Jul 16, 2020
754177d
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lefnelso Jul 16, 2020
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lefnelso Jul 16, 2020
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lefnelso Jul 16, 2020
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lefnelso Jul 16, 2020
1e0cf3e
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lefnelso Jul 16, 2020
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lefnelso Jul 16, 2020
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lefnelso Jul 16, 2020
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lefnelso Jul 16, 2020
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lefnelso Jul 16, 2020
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lefnelso Jul 16, 2020
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lefnelso Jul 16, 2020
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lefnelso Jul 16, 2020
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lefnelso Jul 16, 2020
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lefnelso Jul 16, 2020
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lefnelso Jul 16, 2020
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lefnelso Jul 16, 2020
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lefnelso Jul 16, 2020
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adding all edges v all edges
ppxasjsm Aug 20, 2020
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polishing all edge statistics
ppxasjsm Aug 20, 2020
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lefnelso Aug 25, 2020
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lefnelso Aug 25, 2020
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lefnelso Aug 25, 2020
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Create readme for protein amber files
SofiaBariami Aug 28, 2020
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1 change: 1 addition & 0 deletions QuBe-SOMD_paper/FEP_preparation/Complex/README.md
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Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
Complex (ligand bound to protein) files
96 changes: 96 additions & 0 deletions QuBe-SOMD_paper/FEP_preparation/Ligands/Lig1.pdb
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Original file line number Diff line number Diff line change
@@ -0,0 +1,96 @@
REMARK LIGPARGEN GENERATED PDB FILE
ATOM 1 N00 29T 1 497.653 -25.281 29.629
ATOM 2 C01 29T 1 497.062 -24.788 28.769
ATOM 3 C02 29T 1 496.319 -24.169 27.689
ATOM 4 C03 29T 1 496.123 -24.799 26.442
ATOM 5 C04 29T 1 495.660 -22.961 27.678
ATOM 6 H05 29T 1 496.534 -25.781 26.264
ATOM 7 C06 29T 1 495.354 -23.904 25.640
ATOM 8 H07 29T 1 495.658 -22.339 28.561
ATOM 9 N08 29T 1 495.091 -22.776 26.431
ATOM 10 C09 29T 1 494.816 -23.866 24.309
ATOM 11 C0A 29T 1 494.380 -21.652 26.051
ATOM 12 O0B 29T 1 495.067 -24.970 23.514
ATOM 13 C0C 29T 1 494.073 -22.717 23.900
ATOM 14 H0D 29T 1 494.239 -20.841 26.750
ATOM 15 C0E 29T 1 493.870 -21.586 24.797
ATOM 16 C0F 29T 1 495.184 -24.835 22.148
ATOM 17 H0G 29T 1 493.650 -22.673 22.908
ATOM 18 H0H 29T 1 493.324 -20.709 24.482
ATOM 19 C0I 29T 1 494.115 -25.249 21.300
ATOM 20 C0J 29T 1 496.369 -24.286 21.590
ATOM 21 O0K 29T 1 492.995 -25.775 21.906
ATOM 22 C0M 29T 1 494.242 -25.109 19.892
ATOM 23 H0N 29T 1 497.175 -23.975 22.236
ATOM 24 C0O 29T 1 496.480 -24.150 20.193
ATOM 25 C0P 29T 1 491.839 -26.148 21.158
ATOM 26 H0Q 29T 1 493.442 -25.419 19.236
ATOM 27 C0R 29T 1 495.422 -24.560 19.355
ATOM 28 H0S 29T 1 497.378 -23.732 19.763
ATOM 29 C0T 29T 1 491.047 -27.143 22.037
ATOM 30 H0U 29T 1 492.149 -26.644 20.239
ATOM 31 H0V 29T 1 491.229 -25.264 20.972
ATOM 32 N0W 29T 1 491.830 -28.285 22.587
ATOM 33 H0X 29T 1 490.199 -27.526 21.471
ATOM 34 H0Y 29T 1 490.577 -26.601 22.858
ATOM 35 C0Z 29T 1 492.363 -28.073 23.892
ATOM 36 C10 29T 1 492.051 -29.478 21.928
ATOM 37 H11 29T 1 492.185 -27.138 24.402
ATOM 38 C12 29T 1 493.096 -29.034 24.512
ATOM 39 O13 29T 1 491.624 -29.733 20.806
ATOM 40 N14 29T 1 492.789 -30.405 22.591
ATOM 41 H15 29T 1 493.497 -28.866 25.500
ATOM 42 C16 29T 1 493.339 -30.304 23.827
ATOM 43 H17 29T 1 492.985 -31.296 22.159
ATOM 44 O18 29T 1 493.987 -31.227 24.312
ATOM 45 H19 29T 1 495.510 -24.454 18.284
TER
CONECT 1 2
CONECT 2 3
CONECT 3 4
CONECT 3 5
CONECT 4 6
CONECT 4 7
CONECT 5 8
CONECT 5 9
CONECT 7 10
CONECT 9 11
CONECT 10 12
CONECT 10 13
CONECT 11 14
CONECT 11 15
CONECT 12 16
CONECT 13 17
CONECT 15 18
CONECT 16 19
CONECT 16 20
CONECT 19 21
CONECT 19 22
CONECT 20 23
CONECT 20 24
CONECT 21 25
CONECT 22 26
CONECT 22 27
CONECT 24 28
CONECT 25 29
CONECT 25 30
CONECT 25 31
CONECT 29 32
CONECT 29 33
CONECT 29 34
CONECT 32 35
CONECT 32 36
CONECT 35 37
CONECT 35 38
CONECT 36 39
CONECT 36 40
CONECT 38 41
CONECT 38 42
CONECT 40 43
CONECT 42 44
CONECT 27 45
CONECT 7 9
CONECT 13 15
CONECT 24 27
CONECT 40 42
END
460 changes: 460 additions & 0 deletions QuBe-SOMD_paper/FEP_preparation/Ligands/Lig1.xml
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Large diffs are not rendered by default.

96 changes: 96 additions & 0 deletions QuBe-SOMD_paper/FEP_preparation/Ligands/Lig10.pdb
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,96 @@
REMARK LIGPARGEN GENERATED PDB FILE
ATOM 1 N00 29T 1 497.651 -25.282 29.630
ATOM 2 C01 29T 1 497.060 -24.788 28.770
ATOM 3 C02 29T 1 496.318 -24.169 27.690
ATOM 4 C03 29T 1 496.122 -24.800 26.442
ATOM 5 N04 29T 1 495.659 -22.961 27.678
ATOM 6 H05 29T 1 496.533 -25.782 26.264
ATOM 7 C06 29T 1 495.354 -23.904 25.641
ATOM 8 H07 29T 1 495.657 -22.379 28.504
ATOM 9 C08 29T 1 495.090 -22.776 26.431
ATOM 10 C09 29T 1 494.816 -23.866 24.309
ATOM 11 C0A 29T 1 494.380 -21.652 26.051
ATOM 12 O0B 29T 1 495.067 -24.970 23.514
ATOM 13 C0C 29T 1 494.073 -22.717 23.900
ATOM 14 H0D 29T 1 494.239 -20.841 26.750
ATOM 15 C0E 29T 1 493.870 -21.586 24.797
ATOM 16 C0F 29T 1 495.184 -24.835 22.148
ATOM 17 H0G 29T 1 493.650 -22.673 22.908
ATOM 18 H0H 29T 1 493.325 -20.708 24.482
ATOM 19 C0I 29T 1 494.115 -25.249 21.300
ATOM 20 C0J 29T 1 496.369 -24.286 21.590
ATOM 21 O0K 29T 1 492.995 -25.775 21.906
ATOM 22 C0M 29T 1 494.243 -25.109 19.892
ATOM 23 H0N 29T 1 497.176 -23.975 22.237
ATOM 24 C0O 29T 1 496.481 -24.150 20.194
ATOM 25 C0P 29T 1 491.839 -26.148 21.158
ATOM 26 H0Q 29T 1 493.443 -25.419 19.236
ATOM 27 C0R 29T 1 495.423 -24.560 19.356
ATOM 28 H0S 29T 1 497.379 -23.732 19.764
ATOM 29 C0T 29T 1 491.047 -27.142 22.037
ATOM 30 H0U 29T 1 492.149 -26.644 20.238
ATOM 31 H0V 29T 1 491.229 -25.264 20.971
ATOM 32 N0W 29T 1 491.829 -28.284 22.586
ATOM 33 H0X 29T 1 490.199 -27.525 21.470
ATOM 34 H0Y 29T 1 490.577 -26.600 22.857
ATOM 35 C0Z 29T 1 492.363 -28.072 23.892
ATOM 36 C10 29T 1 492.050 -29.477 21.927
ATOM 37 H11 29T 1 492.185 -27.137 24.402
ATOM 38 C12 29T 1 493.095 -29.034 24.512
ATOM 39 O13 29T 1 491.623 -29.732 20.805
ATOM 40 N14 29T 1 492.788 -30.404 22.591
ATOM 41 H15 29T 1 493.496 -28.866 25.500
ATOM 42 C16 29T 1 493.338 -30.303 23.827
ATOM 43 H17 29T 1 492.984 -31.296 22.159
ATOM 44 O18 29T 1 493.986 -31.226 24.312
ATOM 45 H19 29T 1 495.511 -24.454 18.284
TER
CONECT 1 2
CONECT 2 3
CONECT 3 4
CONECT 3 5
CONECT 4 6
CONECT 4 7
CONECT 5 8
CONECT 5 9
CONECT 7 10
CONECT 9 11
CONECT 10 12
CONECT 10 13
CONECT 11 14
CONECT 11 15
CONECT 12 16
CONECT 13 17
CONECT 15 18
CONECT 16 19
CONECT 16 20
CONECT 19 21
CONECT 19 22
CONECT 20 23
CONECT 20 24
CONECT 21 25
CONECT 22 26
CONECT 22 27
CONECT 24 28
CONECT 25 29
CONECT 25 30
CONECT 25 31
CONECT 29 32
CONECT 29 33
CONECT 29 34
CONECT 32 35
CONECT 32 36
CONECT 35 37
CONECT 35 38
CONECT 36 39
CONECT 36 40
CONECT 38 41
CONECT 38 42
CONECT 40 43
CONECT 42 44
CONECT 27 45
CONECT 7 9
CONECT 13 15
CONECT 24 27
CONECT 40 42
END
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