- Posts: 4
CG MD for new Molecule
- Shadman Lakmehsari
-
Topic Author
- Offline
- Fresh Boarder
Less
More
2 years 9 months ago #9070
by Shadman Lakmehsari
CG MD for new Molecule was created by Shadman Lakmehsari
I have been attempting to run the CG mapping a new molecule, named Tween21 from
cgmartini.nl/index.php/martini-3-tutoria...-molecule-binding#1A
.
SMILES key of Tween21:
CCCCCCCCCCCC(=O)OCCOCC(OCCOC)C1OCC(OCCOC)C1OCCOC
I have been tried to obtain the CG map from auto_martini-main, however, it has strange error:
$ python -m auto_martini --smi "CCCCCCCCCCCC(=O)OCCOCC(OCCOC)C1OCC(OCCOC)C1OCCOC" --mol GUA --cg gua.gro --top GUA.itp
Traceback (most recent call last):
File "/home/muhammad/anaconda3/lib/python3.7/runpy.py", line 183, in _run_module_as_main
mod_name, mod_spec, code = _get_module_details(mod_name, _Error)
File "/home/muhammad/anaconda3/lib/python3.7/runpy.py", line 142, in _get_module_details
return _get_module_details(pkg_main_name, error)
File "/home/muhammad/anaconda3/lib/python3.7/runpy.py", line 109, in _get_module_details
__import__(pkg_name)
File "/home/muhammad/anaconda3/lib/python3.7/site-packages/auto_martini/__init__.py", line 29, in <module>
from . import solver, topology
File "/home/muhammad/anaconda3/lib/python3.7/site-packages/auto_martini/solver.py", line 29, in <module>
from .common import *
File "/home/muhammad/anaconda3/lib/python3.7/site-packages/auto_martini/common.py", line 42, in <module>
from rdkit import Chem
ImportError: cannot import name 'Chem' from 'rdkit' (unknown location)
=====================
anyway I do not know why auto_martini does not work!
In addition, I had many efforts to map by " jbarnoud.github.io/cgbuilder/ "
the results are here:
====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
==============================================
/SNa-SNa
I know the map is C1-C1-C2-Na-SNa-SNa-SNa
\SNa-SNa
(SNa is COC)
Now, how can I proceed the work to generate?
Best,
Muhammad
SMILES key of Tween21:
CCCCCCCCCCCC(=O)OCCOCC(OCCOC)C1OCC(OCCOC)C1OCCOC
I have been tried to obtain the CG map from auto_martini-main, however, it has strange error:
$ python -m auto_martini --smi "CCCCCCCCCCCC(=O)OCCOCC(OCCOC)C1OCC(OCCOC)C1OCCOC" --mol GUA --cg gua.gro --top GUA.itp
Traceback (most recent call last):
File "/home/muhammad/anaconda3/lib/python3.7/runpy.py", line 183, in _run_module_as_main
mod_name, mod_spec, code = _get_module_details(mod_name, _Error)
File "/home/muhammad/anaconda3/lib/python3.7/runpy.py", line 142, in _get_module_details
return _get_module_details(pkg_main_name, error)
File "/home/muhammad/anaconda3/lib/python3.7/runpy.py", line 109, in _get_module_details
__import__(pkg_name)
File "/home/muhammad/anaconda3/lib/python3.7/site-packages/auto_martini/__init__.py", line 29, in <module>
from . import solver, topology
File "/home/muhammad/anaconda3/lib/python3.7/site-packages/auto_martini/solver.py", line 29, in <module>
from .common import *
File "/home/muhammad/anaconda3/lib/python3.7/site-packages/auto_martini/common.py", line 42, in <module>
from rdkit import Chem
ImportError: cannot import name 'Chem' from 'rdkit' (unknown location)
=====================
anyway I do not know why auto_martini does not work!
In addition, I had many efforts to map by " jbarnoud.github.io/cgbuilder/ "
the results are here:
====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
==============================================
/SNa-SNa
I know the map is C1-C1-C2-Na-SNa-SNa-SNa
\SNa-SNa
(SNa is COC)
Now, how can I proceed the work to generate?
Best,
Muhammad
Please Log in or Create an account to join the conversation.
- vainikka
-
- Offline
- Admin
Less
More
- Posts: 91
2 years 9 months ago #9072
by vainikka
Replied by vainikka on topic CG MD for new Molecule
We do not maintain or develop auto_martini, so you will need to go ask about it on their respective website.
As for mapping the molecule yourself, look at the other Martini 3 tutorial,"Parameterization of a small molecule".
As for mapping the molecule yourself, look at the other Martini 3 tutorial,"Parameterization of a small molecule".
Please Log in or Create an account to join the conversation.
Time to create page: 0.099 seconds