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Adding a collection with the ligands of Souza et al., Nat. Commun. 2020 #30

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Adding a collection with the ligands of Souza et al., Nat. Commun. 2020 #30

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88e7f26
Kicstart martini_v3.0.0_small_molecules_2020PCTSouzaNatCommun.itp col…
ricalessandri Apr 26, 2023
baf4f7c
Add also: BENZ, PHEN, TOLU, INDO (completing SI Fig 1 of 2020PCTSouza…
ricalessandri Apr 28, 2023
e773a17
Add BARICITINIB
ricalessandri Apr 28, 2023
d927603
Add ADENOSINE
ricalessandri Apr 28, 2023
df9e900
Add ADRENALINE itp
ricalessandri Apr 28, 2023
05c561b
Add PROPANOLOL
ricalessandri Apr 28, 2023
16a90f4
Add OBETICHOLIC ACID model
ricalessandri Apr 28, 2023
6640e44
Add DASATINIB model
ricalessandri Apr 28, 2023
2b4d234
Move 2020PCTSouzaNatCommun.itp to collections/
ricalessandri May 13, 2023
9492bd3
Add adrenaline GRO file
ricalessandri May 13, 2023
da613e2
Add ADENOSINE gro file
ricalessandri May 13, 2023
af2f1fa
Use beadtype U instead of VS in DASA.itp
ricalessandri May 13, 2023
2113a59
Add GROs of BARI, DASA, OCHO, PRN
ricalessandri May 13, 2023
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11 changes: 11 additions & 0 deletions collections/gros/ADEN.gro
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Original file line number Diff line number Diff line change
@@ -0,0 +1,11 @@
ADEN
8
1ADEN N1 1 1.025 1.049 0.929
1ADEN N2 2 1.158 0.872 1.081
1ADEN N3 3 1.095 0.771 1.286
1ADEN N4 4 0.890 0.817 1.395
1ADEN N5 5 0.841 1.007 1.148
1ADEN C6 6 0.999 0.939 1.115
1ADEN O7 7 0.859 1.229 0.729
1ADEN O8 8 1.049 0.961 0.605
2.00000 2.00000 2.00000
9 changes: 9 additions & 0 deletions collections/gros/ADR.gro
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Original file line number Diff line number Diff line change
@@ -0,0 +1,9 @@
ADR
6
1ADR N1 1 0.938 1.294 1.232
1ADR O2 2 0.896 1.015 1.217
1ADR C3 3 1.025 0.859 1.076
1ADR C4 4 0.830 0.908 0.864
1ADR O5 5 1.048 0.706 0.768
1ADR O6 6 1.171 0.706 0.970
2.00000 2.00000 2.00000
18 changes: 18 additions & 0 deletions collections/gros/BARI.gro
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Original file line number Diff line number Diff line change
@@ -0,0 +1,18 @@
BARI
15
1BARI N1 1 1.204 1.805 1.237
1BARI R2 2 1.391 1.703 1.379
1BARI R3 3 1.229 1.592 1.259
1BARI N4 4 1.077 1.461 1.148
1BARI N5 5 1.243 1.400 1.274
1BARI R6 6 1.475 1.413 1.449
1BARI R7 7 1.359 1.195 1.365
1BARI N8 8 1.523 1.228 1.488
1BARI R9 9 1.753 1.291 1.456
1BARI CN 10 1.923 1.428 1.365
1BARI N11 11 1.697 1.278 1.704
1BARI SOO 12 1.620 1.455 1.852
1BARI C13 13 1.821 1.618 1.744
1BARI U14 14 1.416 1.304 1.407
1BARI U15 15 1.207 1.485 1.245
3.00000 3.00000 3.00000
22 changes: 22 additions & 0 deletions collections/gros/DASA.gro
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Original file line number Diff line number Diff line change
@@ -0,0 +1,22 @@
DASA
19
1DASA R1 1 1.273 2.122 2.472
1DASA R2 2 1.346 1.801 2.316
1DASA Cl 3 1.459 2.222 2.245
1DASA V4 4 1.410 2.039 2.276
1DASA P5 5 1.502 2.000 2.098
1DASA S6 6 1.707 1.857 1.860
1DASA R7 7 1.476 1.933 1.884
1DASA N8 8 1.568 1.867 1.712
1DASA V9 9 1.584 1.886 1.818
1DASA V10 10 1.688 1.805 1.592
1DASA N11 11 1.807 1.795 1.577
1DASA N12 12 1.919 1.577 1.328
1DASA N13 13 2.046 1.799 1.570
1DASA V14 14 1.923 1.723 1.491
1DASA C15 15 2.334 1.663 1.573
1DASA C16 16 2.266 1.955 1.639
1DASA N17 17 2.526 1.836 1.725
1DASA O18 18 2.372 1.668 1.697
1DASA V19 19 2.300 1.809 1.606
3.80000 3.80000 3.80000
12 changes: 12 additions & 0 deletions collections/gros/OCHO.gro
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Original file line number Diff line number Diff line change
@@ -0,0 +1,12 @@
OCHO
9
1OCHO RO1 1 0.708 0.557 1.227
1OCHO R1 2 1.038 0.839 1.470
1OCHO R2 3 1.184 0.431 1.215
1OCHO RO2 4 1.127 0.688 1.023
1OCHO R3 5 0.927 1.035 1.159
1OCHO R4 6 1.291 0.939 0.881
1OCHO R5 7 1.191 1.169 1.100
1OCHO C1 8 1.107 1.344 0.855
1OCHO C2 9 1.220 1.569 0.530
2.00000 2.00000 2.00000
11 changes: 11 additions & 0 deletions collections/gros/PRN.gro
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Original file line number Diff line number Diff line change
@@ -0,0 +1,11 @@
PRN
8
1PRN N1 1 0.649 0.664 1.211
1PRN O2 2 0.790 0.668 0.821
1PRN O3 3 1.042 0.845 0.801
1PRN R4 4 1.062 1.094 0.789
1PRN R5 5 1.125 1.336 0.839
1PRN R6 6 1.209 1.158 0.987
1PRN R7 7 1.298 0.962 1.145
1PRN R8 8 1.351 1.242 1.176
2.00000 2.00000 2.00000
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