normal a new CG model

  • Shadman Lakmehsari
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2 years 11 months ago #9069 by Shadman Lakmehsari
a new CG model was created by Shadman Lakmehsari
I have been attempting to run the "Parametrizing a new molecule" tutorial for Martini3.
cgmartini.nl/index.php/martini-3-tutoria...-molecule-binding#1A .

This Molecule is named Tween21.
Tween21 have generated with Guass-view and optimized with Gaussian. The PDB file extracted and submitted to LIGPARGEN and then the new PDB file used for uploading in jbarnoud.github.io/cgbuilder/ .

The outputs are as follows:


PDB
REMARK LIGPARGEN GENERATED PDB FILE
ATOM 1 H00 H 1 -0.203 0.542 -1.262
ATOM 2 C01 H 1 -0.299 0.458 -0.170
ATOM 3 C02 H 1 0.880 1.133 0.506
ATOM 4 O03 H 1 -1.465 1.110 0.287
ATOM 5 H04 H 1 -0.314 -0.612 0.085
ATOM 6 O05 H 1 2.063 0.460 0.028
ATOM 7 H06 H 1 0.923 2.192 0.250
ATOM 8 H07 H 1 0.814 1.042 1.592
ATOM 9 C08 H 1 3.244 0.910 0.514
ATOM 10 C09 H 1 4.395 0.120 -0.071
ATOM 11 O0A H 1 3.332 1.817 1.300
ATOM 12 C0B H 1 5.764 0.577 0.434
ATOM 13 H0C H 1 4.329 0.198 -1.162
ATOM 14 H0D H 1 4.221 -0.937 0.159
ATOM 15 C0E H 1 6.917 -0.234 -0.165
ATOM 16 H0F H 1 5.894 1.638 0.202
ATOM 17 H0G H 1 5.784 0.504 1.526
ATOM 18 C0H H 1 8.295 0.216 0.332
ATOM 19 H0I H 1 6.885 -0.159 -1.260
ATOM 20 H0J H 1 6.777 -1.297 0.072
ATOM 21 C0K H 1 9.455 -0.591 -0.261
ATOM 22 H0M H 1 8.434 1.278 0.095
ATOM 23 H0N H 1 8.324 0.142 1.427
ATOM 24 C0O H 1 10.833 -0.140 0.235
ATOM 25 H0P H 1 9.423 -0.519 -1.356
ATOM 26 H0Q H 1 9.314 -1.654 -0.022
ATOM 27 C0R H 1 11.994 -0.948 -0.357
ATOM 28 H0S H 1 10.972 0.922 -0.005
ATOM 29 H0T H 1 10.863 -0.211 1.330
ATOM 30 C0U H 1 13.372 -0.495 0.138
ATOM 31 H0V H 1 11.961 -0.876 -1.452
ATOM 32 H0W H 1 11.854 -2.009 -0.115
ATOM 33 C0X H 1 14.533 -1.303 -0.455
ATOM 34 H0Y H 1 13.510 0.567 -0.102
ATOM 35 H0Z H 1 13.404 -0.567 1.233
ATOM 36 C10 H 1 15.911 -0.849 0.038
ATOM 37 H11 H 1 14.498 -1.232 -1.550
ATOM 38 H12 H 1 14.394 -2.365 -0.215
ATOM 39 C13 H 1 17.064 -1.660 -0.561
ATOM 40 H14 H 1 16.048 0.212 -0.202
ATOM 41 H15 H 1 15.943 -0.921 1.132
ATOM 42 H16 H 1 17.078 -1.579 -1.652
ATOM 43 H17 H 1 16.973 -2.721 -0.311
ATOM 44 H18 H 1 18.032 -1.311 -0.191
ATOM 45 C19 H 1 -2.659 0.572 -0.263
ATOM 46 C1A H 1 -3.811 1.471 0.161
ATOM 47 H1B H 1 -2.604 0.558 -1.360
ATOM 48 H1C H 1 -2.811 -0.457 0.086
ATOM 49 C1D H 1 -5.189 0.851 -0.098
ATOM 50 O1E H 1 -3.692 2.684 -0.574
ATOM 51 H1F H 1 -3.712 1.669 1.237
ATOM 52 H1G H 1 -5.310 0.668 -1.171
ATOM 53 O1H H 1 -6.189 1.784 0.341
ATOM 54 C1I H 1 -5.494 -0.453 0.658
ATOM 55 C1J H 1 -3.849 3.880 0.181
ATOM 56 C1K H 1 -7.219 1.110 1.069
ATOM 57 H1M H 1 -5.047 -0.417 1.666
ATOM 58 O1N H 1 -4.992 -1.555 -0.056
ATOM 59 C1O H 1 -7.030 -0.386 0.822
ATOM 60 C1P H 1 -3.683 5.034 -0.790
ATOM 61 H1Q H 1 -4.837 3.922 0.646
ATOM 62 H1R H 1 -3.079 3.946 0.961
ATOM 63 H1S H 1 -8.191 1.466 0.717
ATOM 64 H1T H 1 -7.132 1.342 2.140
ATOM 65 C1U H 1 -5.133 -2.803 0.607
ATOM 66 H1V H 1 -7.390 -0.987 1.665
ATOM 67 O1W H 1 -7.609 -0.818 -0.399
ATOM 68 O1X H 1 -3.834 6.236 -0.056
ATOM 69 H1Y H 1 -4.440 4.961 -1.584
ATOM 70 H1Z H 1 -2.691 4.984 -1.261
ATOM 71 C20 H 1 -3.701 7.388 -0.858
ATOM 72 H21 H 1 -4.464 7.419 -1.652
ATOM 73 H22 H 1 -2.708 7.440 -1.329
ATOM 74 H23 H 1 -3.833 8.253 -0.208
ATOM 75 C24 H 1 -4.486 -3.859 -0.270
ATOM 76 H25 H 1 -6.190 -3.054 0.751
ATOM 77 H26 H 1 -4.643 -2.780 1.591
ATOM 78 C27 H 1 -9.016 -1.043 -0.364
ATOM 79 O28 H 1 -4.682 -5.107 0.363
ATOM 80 H29 H 1 -4.951 -3.841 -1.267
ATOM 81 H2A H 1 -3.414 -3.642 -0.392
ATOM 82 C2B H 1 -4.123 -6.186 -0.358
ATOM 83 H2C H 1 -4.571 -6.277 -1.358
ATOM 84 H2D H 1 -3.035 -6.074 -0.472
ATOM 85 H2E H 1 -4.330 -7.094 0.208
ATOM 86 C2F H 1 -9.332 -2.501 -0.018
ATOM 87 H2G H 1 -9.391 -0.792 -1.358
ATOM 88 H2H H 1 -9.516 -0.383 0.356
ATOM 89 O2I H 1 -10.729 -2.729 0.081
ATOM 90 H2J H 1 -8.872 -3.165 -0.763
ATOM 91 H2K H 1 -8.910 -2.751 0.959
ATOM 92 C2M H 1 -11.363 -3.011 -1.154
ATOM 93 H2N H 1 -11.310 -2.171 -1.858
ATOM 94 H2O H 1 -10.926 -3.898 -1.632
ATOM 95 H2P H 1 -12.413 -3.209 -0.930
TER
CONECT 1 2
CONECT 2 3
CONECT 2 4
CONECT 2 5
CONECT 3 6
CONECT 3 7
CONECT 3 8
CONECT 6 9
CONECT 9 10
CONECT 9 11
CONECT 10 12
CONECT 10 13
CONECT 10 14
CONECT 12 15
CONECT 12 16
CONECT 12 17
CONECT 15 18
CONECT 15 19
CONECT 15 20
CONECT 18 21
CONECT 18 22
CONECT 18 23
CONECT 21 24
CONECT 21 25
CONECT 21 26
CONECT 24 27
CONECT 24 28
CONECT 24 29
CONECT 27 30
CONECT 27 31
CONECT 27 32
CONECT 30 33
CONECT 30 34
CONECT 30 35
CONECT 33 36
CONECT 33 37
CONECT 33 38
CONECT 36 39
CONECT 36 40
CONECT 36 41
CONECT 39 42
CONECT 39 43
CONECT 39 44
CONECT 4 45
CONECT 45 46
CONECT 45 47
CONECT 45 48
CONECT 46 49
CONECT 46 50
CONECT 46 51
CONECT 49 52
CONECT 49 53
CONECT 49 54
CONECT 50 55
CONECT 53 56
CONECT 54 57
CONECT 54 58
CONECT 54 59
CONECT 55 60
CONECT 55 61
CONECT 55 62
CONECT 56 63
CONECT 56 64
CONECT 58 65
CONECT 59 66
CONECT 59 67
CONECT 60 68
CONECT 60 69
CONECT 60 70
CONECT 68 71
CONECT 71 72
CONECT 71 73
CONECT 71 74
CONECT 65 75
CONECT 65 76
CONECT 65 77
CONECT 67 78
CONECT 75 79
CONECT 75 80
CONECT 75 81
CONECT 79 82
CONECT 82 83
CONECT 82 84
CONECT 82 85
CONECT 78 86
CONECT 78 87
CONECT 78 88
CONECT 86 89
CONECT 86 90
CONECT 86 91
CONECT 89 92
CONECT 92 93
CONECT 92 94
CONECT 92 95
CONECT 56 59
END


tween21_cg.gro
Generated with cgbuilder
13
1TN21 B7 1 1.544 -0.109 -0.021
1TN21 B8 2 1.014 -0.037 -0.001
1TN21 B9 3 0.566 0.005 -0.003
1TN21 B10 4 0.188 0.126 0.070
1TN21 B11 5 -0.148 0.031 -0.037
1TN21 B12 6 -0.383 0.293 0.044
1TN21 B13 7 -0.367 0.646 -0.097
1TN21 B14 8 -0.654 0.120 0.050
1TN21 B15 9 -0.420 -0.526 -0.044
1TN21 B16 10 -0.525 -0.184 0.087
1TN21 B17 11 -0.833 -0.073 0.012
1TN21 B18 12 -1.048 -0.293 -0.066
10.00000 10.00000 10.00000

tween21_cg.map

[ to ]
martini

[ martini ]
B7 B8 B9 B10 B11 B12 B13 B14 B15 B16 B17 B18 B19

[ atoms ]
1 H00 B11
2 C01 B11
3 C02 B10
4 O03 B11
5 H04 B11
6 O05 B10
7 H06 B10
8 H07 B10
9 C08 B10
10 C09 B9
11 O0A B10
12 C0B B9
13 H0C B9
14 H0D B9
15 C0E B9
16 H0F B9
17 H0G B9
18 C0H B8
19 H0I B9
20 H0J B9
21 C0K B8
22 H0M B8
23 H0N B8
24 C0O B8
25 H0P B8
26 H0Q B8
27 C0R B8
28 H0S B8
29 H0T B8
30 C0U B7
31 H0V B8
32 H0W B8
33 C0X B7
34 H0Y B7
35 H0Z B7
36 C10 B7
37 H11 B7
38 H12 B7
39 C13 B7
40 H14 B7
41 H15 B7
42 H16 B7
43 H17 B7
44 H18 B7
45 C19 B11
46 C1A B12
47 H1B B11
48 H1C B11
49 C1D B14
50 O1E B12
51 H1F B12
52 H1G B14
53 O1H B14
54 C1I B16
55 C1J B12
56 C1K B14
57 H1M B16
58 O1N B16
59 C1O B17
60 C1P B13
61 H1Q B12
62 H1R B12
63 H1S B14
64 H1T B14
65 C1U B16
66 H1V B17
67 O1W B17
68 O1X B13
69 H1Y B13
70 H1Z B13
71 C20 B13
72 H21 B13
73 H22 B13
74 H23 B13
75 C24 B15
76 H25 B16
77 H26 B16
78 C27 B17
79 O28 B15
80 H29 B15
81 H2A B15
82 C2B B15
83 H2C B15
84 H2D B15
85 H2E B15
86 C2F B18
87 H2G B17
88 H2H B17
89 O2I B18
90 H2J B18
91 H2K B18
92 C2M B18
93 H2N B18
94 H2O B18
95 H2P B18
======================================

tween21_cg.ndx

[ B7 ]
42 43 44 39 41 36 40 38 37 33 35 30 34

[ B8 ]
32 27 31 29 24 28 26 21 25 23 22 18

[ B9 ]
20 15 19 17 12 16 14 10 13

[ B10 ]
11 9 6 3 8 7

[ B11 ]
5 2 1 4 48 45 47

[ B12 ]
51 46 50 61 55 62

[ B13 ]
69 70 60 68 72 71 73 74

[ B14 ]
52 49 53 56 63 64

[ B15 ]
85 84 82 83 79 81 75 80

[ B16 ]
77 65 76 58 57 54

[ B17 ]
66 59 67 88 78 87

[ B18 ]
91 86 90 89 93 92 94 95

========================================

Let me know, what is the next step to generate CG files?
In addition, the CG model and SMILES KEY of Tween21 as follows:
CCCCCCCCCCCC(=O)OCCOCC(OCCOC)C1OCC(OCCOC)C1OCCOC

According to Martini papers, the mapping is
C1-C1-C2-Na-SNa-SNa-SNa-SNa(A)-SNa(A)-SNa(B)-SNa(B)
A is a branch and B is another.

Anyway, Is it necessary to convert Bs (B7-B18) to mapping residue? Really I do not know how we can handle some same residue such as SNa!. I mean here we have 7 SNas, so how we should illustrate each other in ndx and mapping files?

Best,
Muhammad

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2 years 9 months ago #9111 by riccardo
Replied by riccardo on topic a new CG model
Hi,

Not clear if you want to use Martini 2 (the bead type choices you listed) or Martini 3 (the tutorial you linked).
I am assuming you want to use Martini 3.

If so, are you following *this* tutorial
www.cgmartini.nl/index.php/martini-3-tut...a-new-small-molecule
?
because you linked the small-molecule binding tutorial.

Actually, the tutorial about parametrizing small molecules with Martini 3 has just been updated as is available here:
cgmartini.nl/index.php/2021-martini-onli...a-new-small-molecule

I recommend to follow the updated version of the tutorial.

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