[gmx-users] A topol file of calix[4]pyrrole
PeiQuan Chen
gromacs at 163.com
Sat Mar 1 17:02:39 CET 2003
Dear gmx-users(especial Erik,David,Berk)：
Recently I want to do some simulation on the molecule meso-octamethyl-calix[4]pyyrole using the oplsaa force field.Becuase the molecule isn't a potein.So I must be write the top file myself.The following is my building to file of the molecule. Becuase I a newer of this program, I can't confirm whether my .top file is write. So I paste the file in here. If it is someting wrong in it, Please correct it.The .pdb file and .mdp file also gived as a attachment! Thank you!
Ps:When I use the .top file to do EM.And I got a conformation that is not consistent with the literature. In the literature the molecule 1,3-alternative conformation(just like the calix[4]arene ) is a S4 symmetry. But The Gromacs pakages EM result seem the 1,3-alternative distort from the S4 symmetry. Is anything wrong from my .top file!
Here is the calixpyr.top of the molecule(opls_188 atom is a atom type user defined according the literature ):
---Begin of the file
#include "ffoplsaa.itp"
[ moleculetype ]
; Name nrexcl
calix[4]pyrrole 2
[ atoms ]
; nr type resnr residu atom cgnr charge mass
1 opls_545 1 PYR H1 1 0.317 1.0080
2 opls_542 1 PYR N2 1 -0.239 14.0067
3 opls_543 1 PYR C3 1 -0.163 12.0110
4 opls_543 1 PYR C4 1 -0.163 12.0110
5 opls_544 1 PYR C5 1 -0.149 12.0110
6 opls_544 1 PYR C6 1 -0.149 12.0110
7 opls_547 1 PYR H7 1 0.118 1.0080
8 opls_547 1 PYR H8 1 0.118 1.0080
9 opls_118 1 PYR C9 1 0.310 12.0110
10 opls_135 1 PYR C10 2 -0.180 12.0110
11 opls_135 1 PYR C11 3 -0.180 12.0110
12 opls_140 1 PYR H12 2 0.060 1.0080
13 opls_140 1 PYR H13 2 0.060 1.0080
14 opls_140 1 PYR H14 2 0.060 1.0080
15 opls_140 1 PYR H15 3 0.060 1.0080
16 opls_140 1 PYR H16 3 0.060 1.0080
17 opls_140 1 PYR H17 3 0.060 1.0080
18 opls_545 1 PYR H18 4 0.317 1.0080
19 opls_542 1 PYR N19 4 -0.239 14.0067
20 opls_543 1 PYR C20 4 -0.163 12.0110
21 opls_543 1 PYR C21 4 -0.163 12.0110
22 opls_544 1 PYR C22 4 -0.149 12.0110
23 opls_544 1 PYR C23 4 -0.149 12.0110
24 opls_547 1 PYR H24 4 0.118 1.0080
25 opls_547 1 PYR H25 4 0.118 1.0080
26 opls_118 1 PYR C26 4 0.310 12.0110
27 opls_135 1 PYR C27 5 -0.180 12.0110
28 opls_135 1 PYR C28 6 -0.180 12.0110
29 opls_140 1 PYR H29 5 0.060 1.0080
30 opls_140 1 PYR H30 5 0.060 1.0080
31 opls_140 1 PYR H31 5 0.060 1.0080
32 opls_140 1 PYR H32 6 0.060 1.0080
33 opls_140 1 PYR H33 6 0.060 1.0080
34 opls_140 1 PYR H34 6 0.060 1.0080
35 opls_545 1 PYR H35 7 0.317 1.0080
36 opls_542 1 PYR N36 7 -0.239 14.0067
37 opls_543 1 PYR C37 7 -0.163 12.0110
38 opls_543 1 PYR C38 7 -0.163 12.0110
39 opls_544 1 PYR C39 7 -0.149 12.0110
40 opls_544 1 PYR C40 7 -0.149 12.0110
41 opls_547 1 PYR H41 7 0.118 1.0080
42 opls_547 1 PYR H42 7 0.118 1.0080
43 opls_118 1 PYR C43 7 0.310 12.0110
44 opls_135 1 PYR C44 8 -0.180 12.0110
45 opls_135 1 PYR C45 9 -0.180 12.0110
46 opls_140 1 PYR H46 8 0.060 1.0080
47 opls_140 1 PYR H47 8 0.060 1.0080
48 opls_140 1 PYR H48 8 0.060 1.0080
49 opls_140 1 PYR H49 9 0.060 1.0080
50 opls_140 1 PYR H50 9 0.060 1.0080
51 opls_140 1 PYR H51 9 0.060 1.0080
52 opls_545 1 PYR H52 10 0.317 1.0080
53 opls_542 1 PYR N53 10 -0.239 14.0067
54 opls_543 1 PYR C54 10 -0.163 12.0110
55 opls_543 1 PYR C55 10 -0.163 12.0110
56 opls_544 1 PYR C56 10 -0.149 12.0110
57 opls_544 1 PYR C57 10 -0.149 12.0110
58 opls_547 1 PYR H58 10 0.118 1.0080
59 opls_547 1 PYR H59 10 0.118 1.0080
60 opls_118 1 PYR C60 10 0.310 12.0110
61 opls_135 1 PYR C61 11 -0.180 12.0110
62 opls_135 1 PYR C62 12 -0.180 12.0110
63 opls_140 1 PYR H63 11 0.060 1.0080
64 opls_140 1 PYR H64 11 0.060 1.0080
65 opls_140 1 PYR H65 11 0.060 1.0080
66 opls_140 1 PYR H66 12 0.060 1.0080
67 opls_140 1 PYR H67 12 0.060 1.0080
68 opls_140 1 PYR H68 12 0.060 1.0080
[ bonds ]
; ai aj funct b0 kb
1 2 1
2 3 1
2 4 1
3 5 1
3 9 1
4 6 1
4 60 1
5 6 1
5 7 1
6 8 1
9 10 1
9 11 1
9 21 1
10 12 1
10 13 1
10 14 1
11 15 1
11 16 1
11 17 1
18 19 1
19 20 1
19 21 1
20 22 1
20 26 1
21 23 1
22 23 1
22 24 1
23 25 1
26 27 1
26 28 1
26 38 1
27 29 1
27 30 1
27 31 1
28 32 1
28 33 1
28 34 1
35 36 1
36 37 1
36 38 1
37 39 1
37 43 1
38 40 1
39 40 1
39 41 1
40 42 1
43 44 1
43 45 1
43 55 1
44 46 1
44 47 1
44 48 1
45 49 1
45 50 1
45 51 1
52 53 1
53 54 1
53 55 1
54 56 1
54 60 1
55 57 1
56 57 1
56 58 1
57 59 1
60 61 1
60 62 1
61 63 1
61 64 1
61 65 1
62 66 1
62 67 1
62 68 1
[ angles ]
; ai aj ak funct th0 cth
1 2 3 1
1 2 4 1
3 2 4 1
2 3 5 1
2 3 9 1
5 3 9 1
2 4 6 1
2 4 60 1
6 4 60 1
3 5 6 1
3 5 7 1
6 5 7 1
4 6 5 1
4 6 8 1
5 6 8 1
3 9 10 1
3 9 11 1
3 9 21 1 109.500 334.944
10 9 11 1
10 9 21 1
11 9 21 1
9 10 12 1
9 10 13 1
9 10 14 1
12 10 13 1
12 10 14 1
13 10 14 1
9 11 15 1
9 11 16 1
9 11 17 1
15 11 16 1
15 11 17 1
16 11 17 1
18 19 20 1
18 19 21 1
20 19 21 1
19 20 22 1
19 20 26 1
22 20 26 1
9 21 19 1
9 21 23 1
19 21 23 1
20 22 23 1
20 22 24 1
23 22 24 1
21 23 22 1
21 23 25 1
22 23 25 1
20 26 27 1
20 26 28 1
20 26 38 1 109.500 334.944
27 26 28 1
27 26 38 1
28 26 38 1
26 27 29 1
26 27 30 1
26 27 31 1
29 27 30 1
29 27 31 1
30 27 31 1
26 28 32 1
26 28 33 1
26 28 34 1
32 28 33 1
32 28 34 1
33 28 34 1
35 36 37 1
35 36 38 1
37 36 38 1
36 37 39 1
36 37 43 1
39 37 43 1
26 38 36 1
26 38 40 1
36 38 40 1
37 39 40 1
37 39 41 1
40 39 41 1
38 40 39 1
38 40 42 1
39 40 42 1
37 43 44 1
37 43 45 1
37 43 55 1 109.500 334.944
44 43 45 1
44 43 55 1
45 43 55 1
43 44 46 1
43 44 47 1
43 44 48 1
46 44 47 1
46 44 48 1
47 44 48 1
43 45 49 1
43 45 50 1
43 45 51 1
49 45 50 1
49 45 51 1
50 45 51 1
52 53 54 1
52 53 55 1
54 53 55 1
53 54 56 1
53 54 60 1
56 54 60 1
43 55 53 1
43 55 57 1
53 55 57 1
54 56 57 1
54 56 58 1
57 56 58 1
55 57 56 1
55 57 59 1
56 57 59 1
4 60 54 1 109.500 334.944
4 60 61 1
4 60 62 1
54 60 61 1
54 60 62 1
61 60 62 1
60 61 63 1
60 61 64 1
60 61 65 1
63 61 64 1
63 61 65 1
64 61 65 1
60 62 66 1
60 62 67 1
60 62 68 1
66 62 67 1
66 62 68 1
67 62 68 1
[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3 c4 c5
1 2 3 5 3
1 2 3 9 3
4 2 3 5 3
4 2 3 9 3
1 2 4 6 3
1 2 4 60 3
3 2 4 6 3
3 2 4 60 3
2 3 5 6 3
2 3 5 7 3
9 3 5 6 3
9 3 5 7 3
2 3 9 10 3
2 3 9 11 3
2 3 9 21 3 7.15105 2.78004 0.31820 -10.2493 0.00000 0.00000
5 3 9 10 3
5 3 9 11 3
5 3 9 21 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
2 4 6 5 3
2 4 6 8 3
60 4 6 5 3
60 4 6 8 3
2 4 60 54 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
2 4 60 61 3
2 4 60 62 3
6 4 60 54 3 7.15105 2.78004 0.31820 -10.2493 0.00000 0.00000
6 4 60 61 3
6 4 60 62 3
3 5 6 4 3
3 5 6 8 3
7 5 6 4 3
7 5 6 8 3
3 9 10 12 3
3 9 10 13 3
3 9 10 14 3
11 9 10 12 3
11 9 10 13 3
11 9 10 14 3
21 9 10 12 3
21 9 10 13 3
21 9 10 14 3
3 9 11 15 3
3 9 11 16 3
3 9 11 17 3
10 9 11 15 3
10 9 11 16 3
10 9 11 17 3
21 9 11 15 3
21 9 11 16 3
21 9 11 17 3
3 9 21 19 3 7.15105 2.78004 0.31820 -10.2493 0.00000 0.00000
3 9 21 23 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
10 9 21 19 3
10 9 21 23 3
11 9 21 19 3
11 9 21 23 3
18 19 20 22 3
18 19 20 26 3
21 19 20 22 3
21 19 20 26 3
18 19 21 9 3
18 19 21 23 3
20 19 21 9 3
20 19 21 23 3
19 20 22 23 3
19 20 22 24 3
26 20 22 23 3
26 20 22 24 3
19 20 26 27 3
19 20 26 28 3
19 20 26 38 3 7.15105 2.78004 0.31820 -10.2493 0.00000 0.00000
22 20 26 27 3
22 20 26 28 3
22 20 26 38 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
9 21 23 22 3
9 21 23 25 3
19 21 23 22 3
19 21 23 25 3
20 22 23 21 3
20 22 23 25 3
24 22 23 21 3
24 22 23 25 3
20 26 27 29 3
20 26 27 30 3
20 26 27 31 3
28 26 27 29 3
28 26 27 30 3
28 26 27 31 3
38 26 27 29 3
38 26 27 30 3
38 26 27 31 3
20 26 28 32 3
20 26 28 33 3
20 26 28 34 3
27 26 28 32 3
27 26 28 33 3
27 26 28 34 3
38 26 28 32 3
38 26 28 33 3
38 26 28 34 3
20 26 38 36 3 7.15105 2.78004 0.31820 -10.2493 0.00000 0.00000
20 26 38 40 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
27 26 38 36 3
27 26 38 40 3
28 26 38 36 3
28 26 38 40 3
35 36 37 39 3
35 36 37 43 3
38 36 37 39 3
38 36 37 43 3
35 36 38 26 3
35 36 38 40 3
37 36 38 26 3
37 36 38 40 3
36 37 39 40 3
36 37 39 41 3
43 37 39 40 3
43 37 39 41 3
36 37 43 44 3
36 37 43 45 3
36 37 43 55 3 7.15105 2.78004 0.31820 -10.2493 0.00000 0.00000
39 37 43 44 3
39 37 43 45 3
39 37 43 55 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
26 38 40 39 3
26 38 40 42 3
36 38 40 39 3
36 38 40 42 3
37 39 40 38 3
37 39 40 42 3
41 39 40 38 3
41 39 40 42 3
37 43 44 46 3
37 43 44 47 3
37 43 44 48 3
45 43 44 46 3
45 43 44 47 3
45 43 44 48 3
55 43 44 46 3
55 43 44 47 3
55 43 44 48 3
37 43 45 49 3
37 43 45 50 3
37 43 45 51 3
44 43 45 49 3
44 43 45 50 3
44 43 45 51 3
55 43 45 49 3
55 43 45 50 3
55 43 45 51 3
37 43 55 53 3 7.15105 2.78004 0.31820 -10.2493 0.00000 0.00000
37 43 55 57 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
44 43 55 53 3
44 43 55 57 3
45 43 55 53 3
45 43 55 57 3
52 53 54 56 3
52 53 54 60 3
55 53 54 56 3
55 53 54 60 3
52 53 55 43 3
52 53 55 57 3
54 53 55 43 3
54 53 55 57 3
53 54 56 57 3
53 54 56 58 3
60 54 56 57 3
60 54 56 58 3
53 54 60 4 3 7.15105 2.78004 0.31820 -10.2493 0.00000 0.00000
53 54 60 61 3
53 54 60 62 3
56 54 60 4 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
56 54 60 61 3
56 54 60 62 3
43 55 57 56 3
43 55 57 59 3
53 55 57 56 3
53 55 57 59 3
54 56 57 55 3
54 56 57 59 3
58 56 57 55 3
58 56 57 59 3
4 60 61 63 3
4 60 61 64 3
4 60 61 65 3
54 60 61 63 3
54 60 61 64 3
54 60 61 65 3
62 60 61 63 3
62 60 61 64 3
62 60 61 65 3
4 60 62 66 3
4 60 62 67 3
4 60 62 68 3
54 60 62 66 3
54 60 62 67 3
54 60 62 68 3
61 60 62 66 3
61 60 62 67 3
61 60 62 68 3
[ dihedrals ]
; ai aj ak al funct
2 3 4 1 2 improper_Z_N_X_Y
3 5 2 9 2 improper_Z_CA_X_Y
4 2 6 60 2 improper_Z_CA_X_Y
5 6 3 7 2 improper_Z_CA_X_Y
6 4 5 8 2 improper_Z_CA_X_Y
19 20 21 18 2 improper_Z_N_X_Y
20 22 19 26 2 improper_Z_CA_X_Y
21 19 23 9 2 improper_Z_CA_X_Y
22 23 20 24 2 improper_Z_CA_X_Y
23 21 22 25 2 improper_Z_CA_X_Y
36 37 38 35 2 improper_Z_N_X_Y
37 39 36 43 2 improper_Z_CA_X_Y
38 36 40 26 2 improper_Z_CA_X_Y
39 40 37 41 2 improper_Z_CA_X_Y
40 38 39 42 2 improper_Z_CA_X_Y
53 54 55 52 2 improper_Z_N_X_Y
54 56 53 60 2 improper_Z_CA_X_Y
55 53 57 43 2 improper_Z_CA_X_Y
56 57 54 58 2 improper_Z_CA_X_Y
57 55 56 59 2 improper_Z_CA_X_Y
[ system ]
; Name
calix[4]pyrrole
[ molecules ]
; Compound #mols
calix[4]pyrrole 1
----end of the file
Sincerely yours
----
PeiQuan Chen
________________________________________________________________________
PeiQuan Chen Department of Chemistry, Nankai University
WeiJin Road 94, TianJin, 300071, P.R.China
phone: (86)2223506728 Mobile Phone: (+86)13920675030
gromacs at 163.com
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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