Dear all,

i have 1 question,
sorry if the question is little bit silly,

may i know, if we have a system with few compounds meaning, i used packmol to pack all these compounds and run MD simulation until the energy is stable..

if i want to coarse-graining the system,
do i need to re-prepare it and run the MD simulation 1 by 1, then use the trajectory file from this simulation to complete the coarse-graining process(g_fg2cg)
or
i just can use the trajectory from MD simulation of packed structure?

i am a little bit confuse about it, because i have about 11 structure in the system..

Thank you, you reply is greatly appreciated=)

Hi Djurre,

i want to extend the simulation time to until 1000ns, that's why i used CG-MD.

now i get the idea of coarse graining,feel free to correct if there is any mistakes in this protocol;

1. firstly, i skecth the mapped molecules and decided what type of beads that they will be.
2. then, i bulid an itp file based on what we Martini already have (lipids,peo etc..)
3. then i draw pdb structure with the number of atom = no. of beads that we should have in the coarse-grained structure,
4. then do the energy minimization so that the pdb structure will be changed to coarsegrained atomtype (eg: C1,C3,SN0, etc..)

However,
when i run grompp, these error came out;

---

Program grompp, VERSION 4.0
Source code file: toppush.c, line: 897

Fatal error:
Atomtype SCY not found

---

this is my gro file;
UNNAMED
88
1CMP O1A 1 -1.090 0.240 -0.000
1CMP O1A 2 -0.925 0.321 0.000
1CMP O1A 3 -0.776 0.235 -0.000
1CMP O1A 4 -0.624 0.313 -0.000
1CMP O1A 5 -0.439 0.239 -0.000
1CMP O1A 6 -0.307 0.294 -0.000
1CMP O1A 7 -0.123 0.213 -0.000
1CMP O1A 8 0.021 0.293 -0.000
1CMP O1A 9 0.185 0.224 -0.000
1CMP O1A 10 0.326 0.315 -0.000
1CMP O1A 11 0.496 0.224 -0.000
1CMP O1A 12 0.665 0.315 -0.000
1CMP O1A 13 0.832 0.213 -0.000
1CMP O1A 14 0.995 0.317 -0.000
1CMP O1A 15 1.184 0.198 -0.000
1CMP O1A 16 1.323 0.306 -0.000
1CMP O1A 17 1.514 0.189 0.000
1CMP O1A 18 1.668 0.293 0.000
1CMP O1A 19 1.847 0.176 0.000
1CMP O1A 20 2.004 0.293 -0.000
1CMP O1A 21 2.179 0.192 -0.000
1CMP O1A 22 2.323 0.278 -0.000
1CMP O1A 23 2.477 0.179 -0.000
1CMP O1A 24 2.626 0.273 -0.000
1CMP O1A 25 2.796 0.181 -0.000
1CMP O1A 26 2.943 0.299 -0.000
1CMP C1A 27 3.100 0.212 -0.000
1CMP C3A 28 3.278 0.305 0.000
1CMP NaA 29 3.453 0.222 -0.000
1CMP C1A 30 3.599 0.332 -0.000
1CMP O1B 31 -1.081 0.010 -0.000
1CMP O1B 32 -0.925 0.027 0.000
1CMP O1B 33 -0.767 -0.040 -0.000
1CMP O1B 34 -0.613 0.025 -0.000
1CMP O1B 35 -0.437 -0.042 0.000
1CMP O1B 36 -0.268 0.027 0.000
1CMP O1B 37 -0.105 -0.044 0.000
1CMP O1B 38 0.027 0.014 0.000
1CMP O1B 39 0.216 -0.053 0.000
1CMP O1B 40 0.378 0.023 0.000
1CMP O1B 41 0.594 -0.070 0.000
1CMP O1B 42 0.761 -0.001 0.000
1CMP O1B 43 0.939 -0.094 0.000
1CMP O1B 44 1.083 -0.046 -0.000
1CMP O1B 45 1.258 -0.113 0.000
1CMP O1B 46 1.408 -0.051 0.000
1CMP O1B 47 1.577 -0.105 0.000
1CMP O1B 48 1.734 -0.051 0.000
1CMP O1B 49 1.888 -0.128 0.000
1CMP O1B 50 2.029 -0.019 0.000
1CMP O1B 51 2.222 -0.101 0.000
1CMP O1B 52 2.367 -0.021 0.000
1CMP O1B 53 2.547 -0.081 0.000
1CMP O1B 54 2.694 -0.018 0.000
1CMP O1B 55 2.854 -0.115 -0.000
1CMP O1B 56 2.999 -0.049 0.000
1CMP C1B 57 3.155 -0.122 0.000
1CMP C3B 58 3.335 -0.057 0.000
1CMP NaB 59 3.535 -0.146 0.000
1CMP C1B 60 3.672 -0.048 0.000
1CMP O1C 61 -1.082 -0.224 -0.000
1CMP O1C 62 -0.939 -0.299 0.000
1CMP O1C 63 -0.774 -0.248 -0.000
1CMP O1C 64 -0.567 -0.345 -0.000
1CMP O1C 65 -0.400 -0.289 0.000
1CMP O1C 66 -0.216 -0.347 0.000
1CMP O1C 67 -0.086 -0.286 -0.000
1CMP O1C 68 0.109 -0.340 0.000
1CMP O1C 69 0.248 -0.282 0.000
1CMP O1C 70 0.467 -0.368 0.000
1CMP O1C 71 0.615 -0.325 0.000
1CMP O1C 72 0.798 -0.407 -0.000
1CMP O1C 73 0.974 -0.342 0.000
1CMP O1C 74 1.145 -0.420 0.000
1CMP O1C 75 1.310 -0.357 0.000
1CMP O1C 76 1.464 -0.433 0.000
1CMP O1C 77 1.618 -0.375 0.000
1CMP O1C 78 1.783 -0.461 0.000
1CMP O1C 79 1.928 -0.392 0.000
1CMP O1C 80 2.106 -0.463 0.000
1CMP O1C 81 2.293 -0.371 0.000
1CMP O1C 82 2.475 -0.444 0.000
1CMP O1C 83 2.627 -0.364 0.000
1CMP O1C 84 2.828 -0.448 0.000
1CMP C1C 85 2.974 -0.364 0.000
1CMP C3C 86 3.186 -0.454 0.000
1CMP NaC 87 3.356 -0.381 0.000
1CMP C1C 88 3.544 -0.457 0.000
0.00000 0.00000 0.00000

and itp file;
[moleculetype]
;name exclusions
CMP 1


[atoms]
1 SN0 1 CMP O1A 1 0.000 ;
2 SN0 1 CMP O1A 2 0.000 ;
3 SN0 1 CMP O1A 3 0.000 ;
4 SN0 1 CMP O1A 4 0.000 ;
5 SN0 1 CMP O1A 5 0.000 ;
6 SN0 1 CMP O1A 6 0.000 ;
7 SN0 1 CMP O1A 7 0.000 ;
8 SN0 1 CMP O1A 8 0.000 ;
9 SN0 1 CMP O1A 9 0.000 ;
10 SN0 1 CMP O1A 10 0.000 ;
11 SN0 1 CMP O1A 11 0.000 ;
12 SN0 1 CMP O1A 12 0.000 ;
13 SN0 1 CMP O1A 13 0.000 ;
14 SN0 1 CMP O1A 14 0.000 ;
15 SN0 1 CMP O1A 15 0.000 ;
16 SN0 1 CMP O1A 16 0.000 ;
17 SN0 1 CMP O1A 17 0.000 ;
18 SN0 1 CMP O1A 18 0.000 ;
19 SN0 1 CMP O1A 19 0.000 ;
20 SN0 1 CMP O1A 20 0.000 ;
21 SN0 1 CMP O1A 21 0.000 ;
22 SN0 1 CMP O1A 22 0.000 ;
23 SN0 1 CMP O1A 23 0.000 ;
24 SN0 1 CMP O1A 24 0.000 ;
25 SN0 1 CMP O1A 25 0.000 ;
26 SN0 1 CMP O1A 26 0.000 ;
27 C1 1 CMP C1A 27 0.000 ;
28 C3 1 CMP C3A 28 0.000 ;
29 Na 1 CMP NaA 29 0.000 ;
30 C1 1 CMP C1A 30 0.000 ;
1 SN0 1 CMP O1B 31 0.000 ;
2 SN0 1 CMP O1B 32 0.000 ;
3 SN0 1 CMP O1B 33 0.000 ;
4 SN0 1 CMP O1B 34 0.000 ;
5 SN0 1 CMP O1B 35 0.000 ;
6 SN0 1 CMP O1B 36 0.000 ;
7 SN0 1 CMP O1B 37 0.000 ;
8 SN0 1 CMP O1B 38 0.000 ;
9 SN0 1 CMP O1B 39 0.000 ;
10 SN0 1 CMP O1B 40 0.000 ;
11 SN0 1 CMP O1B 41 0.000 ;
12 SN0 1 CMP O1B 42 0.000 ;
13 SN0 1 CMP O1B 43 0.000 ;
14 SN0 1 CMP O1B 44 0.000 ;
15 SN0 1 CMP O1B 45 0.000 ;
16 SN0 1 CMP O1B 46 0.000 ;
17 SN0 1 CMP O1B 47 0.000 ;
18 SN0 1 CMP O1B 48 0.000 ;
19 SN0 1 CMP O1B 49 0.000 ;
20 SN0 1 CMP O1B 50 0.000 ;
21 SN0 1 CMP O1B 51 0.000 ;
22 SN0 1 CMP O1B 52 0.000 ;
23 SN0 1 CMP O1B 53 0.000 ;
24 SN0 1 CMP O1B 54 0.000 ;
25 SN0 1 CMP O1B 55 0.000 ;
26 SN0 1 CMP O1B 56 0.000 ;
27 C1 1 CMP C1B 57 0.000 ;
28 C3 1 CMP C3B 58 0.000 ;
29 Na 1 CMP NaB 59 0.000 ;
30 C1 1 CMP C1B 60 0.000 ;
1 SN0 1 CMP O1C 61 0.000 ;
2 SN0 1 CMP O1C 62 0.000 ;
3 SN0 1 CMP O1C 63 0.000 ;
4 SN0 1 CMP O1C 64 0.000 ;
5 SN0 1 CMP O1C 65 0.000 ;
6 SN0 1 CMP O1C 66 0.000 ;
7 SN0 1 CMP O1C 67 0.000 ;
8 SN0 1 CMP O1C 68 0.000 ;
9 SN0 1 CMP O1C 69 0.000 ;
10 SN0 1 CMP O1C 70 0.000 ;
11 SN0 1 CMP O1C 71 0.000 ;
12 SN0 1 CMP O1C 72 0.000 ;
13 SN0 1 CMP O1C 73 0.000 ;
14 SN0 1 CMP O1C 74 0.000 ;
15 SN0 1 CMP O1C 75 0.000 ;
16 SN0 1 CMP O1C 76 0.000 ;
17 SN0 1 CMP O1C 77 0.000 ;
18 SN0 1 CMP O1C 78 0.000 ;
19 SN0 1 CMP O1C 79 0.000 ;
20 SN0 1 CMP O1C 80 0.000 ;
21 SN0 1 CMP O1C 81 0.000 ;
22 SN0 1 CMP O1C 82 0.000 ;
23 SN0 1 CMP O1C 83 0.000 ;
24 SN0 1 CMP O1C 84 0.000 ;
27 C1 1 CMP C1C 85 0.000 ;
28 C3 1 CMP C3C 86 0.000 ;
29 Na 1 CMP NaC 87 0.000 ;
30 C1 1 CMP C1C 88 0.000 ;



[ bonds ]
;backbonebackbone bonds
1 2 1 0.330 17000 ;
2 3 1 0.330 17000 ;
3 4 1 0.330 17000 ;
4 5 1 0.330 17000 ;
5 6 1 0.330 17000 ;
6 7 1 0.330 17000 ;
7 8 1 0.330 17000 ;
8 9 1 0.330 17000 ;
9 10 1 0.330 17000 ;
10 11 1 0.330 17000 ;
11 12 1 0.330 17000 ;
12 13 1 0.330 17000 ;
13 14 1 0.330 17000 ;
14 15 1 0.330 17000 ;
15 16 1 0.330 17000 ;
16 17 1 0.330 17000 ;
17 18 1 0.330 17000 ;
18 19 1 0.330 17000 ;
19 20 1 0.330 17000 ;
20 21 1 0.330 17000 ;
21 22 1 0.330 17000 ;
22 23 1 0.330 17000 ;
23 24 1 0.330 17000 ;
24 25 1 0.330 17000 ;
25 26 1 0.330 17000 ;
26 27 1 0.330 17000 ;
27 28 1 0.470 1250 ;
28 29 1 0.470 1250 ;
29 30 1 0.470 1250 ;
1 31 1 0.330 17000 ;
31 32 1 0.330 17000 ;
32 33 1 0.330 17000 ;
33 34 1 0.330 17000 ;
34 35 1 0.330 17000 ;
35 36 1 0.330 17000 ;
36 37 1 0.330 17000 ;
37 38 1 0.330 17000 ;
38 39 1 0.330 17000 ;
39 40 1 0.330 17000 ;
40 41 1 0.330 17000 ;
41 42 1 0.330 17000 ;
42 43 1 0.330 17000 ;
43 44 1 0.330 17000 ;
44 45 1 0.330 17000 ;
45 46 1 0.330 17000 ;
46 47 1 0.330 17000 ;
47 48 1 0.330 17000 ;
48 49 1 0.330 17000 ;
49 50 1 0.330 17000 ;
50 51 1 0.330 17000 ;
51 52 1 0.330 17000 ;
52 53 1 0.330 17000 ;
53 54 1 0.330 17000 ;
54 55 1 0.330 17000 ;
55 56 1 0.330 17000 ;
56 57 1 0.330 17000 ;
57 58 1 0.470 1250 ;
58 59 1 0.470 1250 ;
59 60 1 0.470 1250 ;
31 61 1 0.330 17000 ;
61 62 1 0.330 17000 ;
62 63 1 0.330 17000 ;
63 64 1 0.330 17000 ;
64 65 1 0.330 17000 ;
65 66 1 0.330 17000 ;
66 67 1 0.330 17000 ;
67 68 1 0.330 17000 ;
68 69 1 0.330 17000 ;
69 70 1 0.330 17000 ;
70 71 1 0.330 17000 ;
71 72 1 0.330 17000 ;
72 73 1 0.330 17000 ;
73 74 1 0.330 17000 ;
74 75 1 0.330 17000 ;
75 76 1 0.330 17000 ;
76 77 1 0.330 17000 ;
77 78 1 0.330 17000 ;
78 79 1 0.330 17000 ;
79 80 1 0.330 17000 ;
80 81 1 0.330 17000 ;
81 82 1 0.330 17000 ;
82 83 1 0.330 17000 ;
83 84 1 0.330 17000 ;
84 85 1 0.330 17000 ;
85 86 1 0.470 1250 ;
86 87 1 0.470 1250 ;
87 88 1 0.470 1250 ;

[angles]
;backbonebackbonebackbone angles
;
; Note: in the original publication a force constant of 85 was used with a cosine-type angle potential (type 2).
; Numerical stability is improved when a normal harmonic angle potential (type 1) is used with a force constant of 50.
; The two potentials are virtually identical around the equilibrium angle, but the probability density of
; angles around 180 degrees is lowered avoiding problems with the dihedral angles becoming ill-defined.
;
1 2 3 1 130.00 50 ;
2 3 4 1 130.00 50 ;
3 4 5 1 130.00 50 ;
4 5 6 1 130.00 50 ;
5 6 7 1 130.00 50 ;
6 7 8 1 130.00 50 ;
7 8 9 1 130.00 50 ;
8 9 10 1 130.00 50 ;
9 10 11 1 130.00 50 ;
10 11 12 1 130.00 50 ;
11 12 13 1 130.00 50 ;
12 13 14 1 130.00 50 ;
13 14 15 1 130.00 50 ;
14 15 16 1 130.00 50 ;
15 16 17 1 130.00 50 ;
16 17 18 1 130.00 50 ;
17 18 19 1 130.00 50 ;
18 19 20 1 130.00 50 ;
19 20 21 1 130.00 50 ;
20 21 22 1 130.00 50 ;
21 22 23 1 130.00 50 ;
22 23 24 1 130.00 50 ;
23 24 25 1 130.00 50 ;
24 25 26 1 130.00 50 ;
25 26 27 1 130.00 50 ;
26 27 28 1 130.00 50 ;
27 28 29 1 130.00 50 ;
28 29 30 1 130.00 50 ;
31 32 33 1 130.00 50 ;
32 33 34 1 130.00 50 ;
33 34 35 1 130.00 50 ;
34 35 36 1 130.00 50 ;
35 36 37 1 130.00 50 ;
36 37 38 1 130.00 50 ;
37 38 39 1 130.00 50 ;
38 39 40 1 130.00 50 ;
39 40 41 1 130.00 50 ;
40 41 42 1 130.00 50 ;
41 42 43 1 130.00 50 ;
42 43 44 1 130.00 50 ;
43 44 45 1 130.00 50 ;
44 45 46 1 130.00 50 ;
45 46 47 1 130.00 50 ;
46 47 48 1 130.00 50 ;
47 48 49 1 130.00 50 ;
48 49 50 1 130.00 50 ;
49 50 51 1 130.00 50 ;
50 51 52 1 130.00 50 ;
51 52 53 1 130.00 50 ;
52 53 54 1 130.00 50 ;
53 54 55 1 130.00 50 ;
54 55 56 1 130.00 50 ;
55 56 57 1 130.00 50 ;
56 57 58 1 130.00 50 ;
57 58 59 1 130.00 50 ;
58 59 60 1 130.00 50 ;
61 62 63 1 130.00 50 ;
62 63 64 1 130.00 50 ;
63 64 65 1 130.00 50 ;
64 65 66 1 130.00 50 ;
65 66 67 1 130.00 50 ;
66 67 68 1 130.00 50 ;
67 68 69 1 130.00 50 ;
68 69 70 1 130.00 50 ;
69 70 71 1 130.00 50 ;
70 71 72 1 130.00 50 ;
71 72 73 1 130.00 50 ;
72 73 74 1 130.00 50 ;
73 74 75 1 130.00 50 ;
74 75 76 1 130.00 50 ;
75 76 77 1 130.00 50 ;
76 77 78 1 130.00 50 ;
77 78 79 1 130.00 50 ;
78 79 80 1 130.00 50 ;
79 80 81 1 130.00 50 ;
80 81 82 1 130.00 50 ;
81 82 83 1 130.00 50 ;
82 83 84 1 130.00 50 ;
83 84 85 1 130.00 50 ;
84 85 86 1 130.00 50 ;
85 86 87 1 130.00 50 ;
86 87 88 1 130.00 50 ;
1 31 61 1 130.00 50 ;


[dihedrals]
1 2 3 4 1 180.00 1.96 1
1 2 3 4 1 0 0.18 2
1 2 3 4 1 0 0.33 3
1 2 3 4 1 0 0.12 4
2 3 4 5 1 180.00 1.96 1
2 3 4 5 1 0 0.18 2
2 3 4 5 1 0 0.33 3
2 3 4 5 1 0 0.12 4
3 4 5 6 1 180.00 1.96 1
3 4 5 6 1 0 0.18 2
3 4 5 6 1 0 0.33 3
3 4 5 6 1 0 0.12 4
4 5 6 7 1 180.00 1.96 1
4 5 6 7 1 0 0.18 2
4 5 6 7 1 0 0.33 3
4 5 6 7 1 0 0.12 4
5 6 7 8 1 180.00 1.96 1
5 6 7 8 1 0 0.18 2
5 6 7 8 1 0 0.33 3
5 6 7 8 1 0 0.12 4
6 7 8 9 1 180.00 1.96 1
6 7 8 9 1 0 0.18 2
6 7 8 9 1 0 0.33 3
6 7 8 9 1 0 0.12 4
7 8 9 10 1 180.00 1.96 1
7 8 9 10 1 0 0.18 2
7 8 9 10 1 0 0.33 3
7 8 9 10 1 0 0.12 4
8 9 10 11 1 180.00 1.96 1
8 9 10 11 1 0 0.18 2
8 9 10 11 1 0 0.33 3
8 9 10 11 1 0 0.12 4
9 10 11 12 1 180.00 1.96 1
9 10 11 12 1 0 0.18 2
9 10 11 12 1 0 0.33 3
9 10 11 12 1 0 0.12 4
10 11 12 13 1 180.00 1.96 1
10 11 12 13 1 0 0.18 2
10 11 12 13 1 0 0.33 3
10 11 12 13 1 0 0.12 4
11 12 13 14 1 180.00 1.96 1
11 12 13 14 1 0 0.18 2
11 12 13 14 1 0 0.33 3
11 12 13 14 1 0 0.12 4
12 13 14 15 1 180.00 1.96 1
12 13 14 15 1 0 0.18 2
12 13 14 15 1 0 0.33 3
12 13 14 15 1 0 0.12 4
13 14 15 16 1 180.00 1.96 1
13 14 15 16 1 0 0.18 2
13 14 15 16 1 0 0.33 3
13 14 15 16 1 0 0.12 4
14 15 16 17 1 180.00 1.96 1
14 15 16 17 1 0 0.18 2
14 15 16 17 1 0 0.33 3
14 15 16 17 1 0 0.12 4
15 16 17 18 1 180.00 1.96 1
15 16 17 18 1 0 0.18 2
15 16 17 18 1 0 0.33 3
15 16 17 18 1 0 0.12 4
16 17 18 19 1 180.00 1.96 1
16 17 18 19 1 0 0.18 2
16 17 18 19 1 0 0.33 3
16 17 18 19 1 0 0.12 4
17 18 19 20 1 180.00 1.96 1
17 18 19 20 1 0 0.18 2
17 18 19 20 1 0 0.33 3
17 18 19 20 1 0 0.12 4
18 19 20 21 1 180.00 1.96 1
18 19 20 21 1 0 0.18 2
18 19 20 21 1 0 0.33 3
18 19 20 21 1 0 0.12 4
19 20 21 22 1 180.00 1.96 1
19 20 21 22 1 0 0.18 2
19 20 21 22 1 0 0.33 3
19 20 21 22 1 0 0.12 4
20 21 22 23 1 180.00 1.96 1
20 21 22 23 1 0 0.18 2
20 21 22 23 1 0 0.33 3
20 21 22 23 1 0 0.12 4
21 22 23 24 1 180.00 1.96 1
21 22 23 24 1 0 0.18 2
21 22 23 24 1 0 0.33 3
21 22 23 24 1 0 0.12 4
22 23 24 25 1 180.00 1.96 1
22 23 24 25 1 0 0.18 2
22 23 24 25 1 0 0.33 3
22 23 24 25 1 0 0.12 4
23 24 25 26 1 180.00 1.96 1
23 24 25 26 1 0 0.18 2
23 24 25 26 1 0 0.33 3
23 24 25 26 1 0 0.12 4
31 32 33 34 1 180.00 1.96 1
31 32 33 34 1 0 0.18 2
31 32 33 34 1 0 0.33 3
31 32 33 34 1 0 0.12 4
32 33 34 35 1 180.00 1.96 1
32 33 34 35 1 0 0.18 2
32 33 34 35 1 0 0.33 3
32 33 34 35 1 0 0.12 4
33 34 35 36 1 180.00 1.96 1
33 34 35 36 1 0 0.18 2
33 34 35 36 1 0 0.33 3
33 34 35 36 1 0 0.12 4
34 35 36 37 1 180.00 1.96 1
34 35 36 37 1 0 0.18 2
34 35 36 37 1 0 0.33 3
34 35 36 37 1 0 0.12 4
35 36 37 38 1 180.00 1.96 1
35 36 37 38 1 0 0.18 2
35 36 37 38 1 0 0.33 3
35 36 37 38 1 0 0.12 4
36 37 38 39 1 180.00 1.96 1
36 37 38 39 1 0 0.18 2
36 37 38 39 1 0 0.33 3
36 37 38 39 1 0 0.12 4
37 38 39 40 1 180.00 1.96 1
37 38 39 40 1 0 0.18 2
37 38 39 40 1 0 0.33 3
37 38 39 40 1 0 0.12 4
38 39 40 41 1 180.00 1.96 1
38 39 40 41 1 0 0.18 2
38 39 40 41 1 0 0.33 3
38 39 40 41 1 0 0.12 4
39 40 41 42 1 180.00 1.96 1
39 40 41 42 1 0 0.18 2
39 40 41 42 1 0 0.33 3
39 40 41 42 1 0 0.12 4
40 41 42 43 1 180.00 1.96 1
40 41 42 43 1 0 0.18 2
40 41 42 43 1 0 0.33 3
40 41 42 43 1 0 0.12 4
41 42 43 44 1 180.00 1.96 1
41 42 43 44 1 0 0.18 2
41 42 43 44 1 0 0.33 3
41 42 43 44 1 0 0.12 4
42 43 44 45 1 180.00 1.96 1
42 43 44 45 1 0 0.18 2
42 43 44 45 1 0 0.33 3
42 43 44 45 1 0 0.12 4
43 44 45 46 1 180.00 1.96 1
43 44 45 46 1 0 0.18 2
43 44 45 46 1 0 0.33 3
43 44 45 46 1 0 0.12 4
44 45 46 47 1 180.00 1.96 1
44 45 46 47 1 0 0.18 2
44 45 46 47 1 0 0.33 3
44 45 46 47 1 0 0.12 4
45 46 47 48 1 180.00 1.96 1
45 46 47 48 1 0 0.18 2
45 46 47 48 1 0 0.33 3
45 46 47 48 1 0 0.12 4
46 47 48 49 1 180.00 1.96 1
46 47 48 49 1 0 0.18 2
46 47 48 49 1 0 0.33 3
46 47 48 49 1 0 0.12 4
47 48 49 50 1 180.00 1.96 1
47 48 49 50 1 0 0.18 2
47 48 49 50 1 0 0.33 3
47 48 49 50 1 0 0.12 4
48 49 50 51 1 180.00 1.96 1
48 49 50 51 1 0 0.18 2
48 49 50 51 1 0 0.33 3
48 49 50 51 1 0 0.12 4
49 50 51 52 1 180.00 1.96 1
49 50 51 52 1 0 0.18 2
49 50 51 52 1 0 0.33 3
49 50 51 52 1 0 0.12 4
50 51 52 53 1 180.00 1.96 1
50 51 52 53 1 0 0.18 2
50 51 52 53 1 0 0.33 3
50 51 52 53 1 0 0.12 4
51 52 53 54 1 180.00 1.96 1
51 52 53 54 1 0 0.18 2
51 52 53 54 1 0 0.33 3
51 52 53 54 1 0 0.12 4
52 53 54 55 1 180.00 1.96 1
52 53 54 55 1 0 0.18 2
52 53 54 55 1 0 0.33 3
52 53 54 55 1 0 0.12 4
53 54 55 56 1 180.00 1.96 1
53 54 55 56 1 0 0.18 2
53 54 55 56 1 0 0.33 3
53 54 55 56 1 0 0.12 4
61 62 63 64 1 180.00 1.96 1
61 62 63 64 1 0 0.18 2
61 62 63 64 1 0 0.33 3
61 62 63 64 1 0 0.12 4
62 63 64 65 1 180.00 1.96 1
62 63 64 65 1 0 0.18 2
62 63 64 65 1 0 0.33 3
62 63 64 65 1 0 0.12 4
63 64 65 66 1 180.00 1.96 1
63 64 65 66 1 0 0.18 2
63 64 65 66 1 0 0.33 3
63 64 65 66 1 0 0.12 4
64 65 66 67 1 180.00 1.96 1
64 65 66 67 1 0 0.18 2
64 65 66 67 1 0 0.33 3
64 65 66 67 1 0 0.12 4
65 66 67 68 1 180.00 1.96 1
65 66 67 68 1 0 0.18 2
65 66 67 68 1 0 0.33 3
65 66 67 68 1 0 0.12 4
66 67 68 69 1 180.00 1.96 1
66 67 68 69 1 0 0.18 2
66 67 68 69 1 0 0.33 3
66 67 68 69 1 0 0.12 4
67 68 69 70 1 180.00 1.96 1
67 68 69 70 1 0 0.18 2
67 68 69 70 1 0 0.33 3
67 68 69 70 1 0 0.12 4
68 69 70 71 1 180.00 1.96 1
68 69 70 71 1 0 0.18 2
68 69 70 71 1 0 0.33 3
68 69 70 71 1 0 0.12 4
69 70 71 72 1 180.00 1.96 1
69 70 71 72 1 0 0.18 2
69 70 71 72 1 0 0.33 3
69 70 71 72 1 0 0.12 4
70 71 72 73 1 180.00 1.96 1
70 71 72 73 1 0 0.18 2
70 71 72 73 1 0 0.33 3
70 71 72 73 1 0 0.12 4
71 72 73 74 1 180.00 1.96 1
71 72 73 74 1 0 0.18 2
71 72 73 74 1 0 0.33 3
71 72 73 74 1 0 0.12 4
72 73 74 75 1 180.00 1.96 1
72 73 74 75 1 0 0.18 2
72 73 74 75 1 0 0.33 3
72 73 74 75 1 0 0.12 4
73 74 75 76 1 180.00 1.96 1
73 74 75 76 1 0 0.18 2
73 74 75 76 1 0 0.33 3
73 74 75 76 1 0 0.12 4
74 75 76 77 1 180.00 1.96 1
74 75 76 77 1 0 0.18 2
74 75 76 77 1 0 0.33 3
74 75 76 77 1 0 0.12 4
75 76 77 78 1 180.00 1.96 1
75 76 77 78 1 0 0.18 2
75 76 77 78 1 0 0.33 3
75 76 77 78 1 0 0.12 4
76 77 78 79 1 180.00 1.96 1
76 77 78 79 1 0 0.18 2
76 77 78 79 1 0 0.33 3
76 77 78 79 1 0 0.12 4
77 78 79 80 1 180.00 1.96 1
77 78 79 80 1 0 0.18 2
77 78 79 80 1 0 0.33 3
77 78 79 80 1 0 0.12 4
78 79 80 81 1 180.00 1.96 1
78 79 80 81 1 0 0.18 2
78 79 80 81 1 0 0.33 3
78 79 80 81 1 0 0.12 4
79 80 81 82 1 180.00 1.96 1
79 80 81 22 1 0 0.18 2
79 80 81 82 1 0 0.33 3
79 80 81 82 1 0 0.12 4
80 81 82 83 1 180.00 1.96 1
80 81 82 83 1 0 0.18 2
80 81 82 83 1 0 0.33 3
80 81 82 83 1 0 0.12 4
81 82 83 84 1 180.00 1.96 1
81 82 83 84 1 0 0.18 2
81 82 83 84 1 0 0.33 3
81 82 83 84 1 0 0.12 4

top file;
#include "martini_v2.0.itp"
#include "martini_v2.0_polymers.itp"
#include "martini_v2.0_lipids.itp"
#include "CMP.itp"

[ system ]
; Name
CMP molecules in water

[ molecules ]
; Compound #mols
CMP 1
W 12434

grompp -f em.mdp -c cmp-wat.gro -p cmp.top -o em.tpr

i checked all the files included in this command, however, i couldn't find any SCY type and even i checked [moleculetype] and [atomtype] parts in all .itp files, and they all are consistent with my previous simulation run (DPPC in water)....

does you know where is the source of this error actually?

you reply is greatly appreciated..

Thank you so much..

Hi Djurre,

sorry for bothering you,

i solved the problem!=)
thank you=)