GROMACS version:2016.4
ERROR 1 [file glc.itp, line 1074]:
No default Proper Dih. types
ERROR 2 [file glc.itp, line 1110]:
No default Proper Dih. types
ERROR 3 [file glc.itp, line 1140]:
No default Proper Dih. types
ERROR 4 [file glc.itp, line 1170]:
No default Proper Dih. types
ERROR 5 [file glc.itp, line 1201]:
No default Proper Dih. types
ERROR 6 [file glc.itp, line 1245]:
No default Proper Dih. types
ERROR 7 [file glc.itp, line 1269]:
No default Proper Dih. types
ERROR 8 [file glc.itp, line 1307]:
No default Proper Dih. types
ERROR 9 [file glc.itp, line 1337]:
No default Proper Dih. types
ERROR 10 [file glc.itp, line 1374]:
No default Proper Dih. types
ERROR 11 [file glc.itp, line 1402]:
No default Proper Dih. types
ERROR 12 [file glc.itp, line 1443]:
No default Proper Dih. types
ERROR 13 [file glc.itp, line 1467]:
No default Proper Dih. types
ERROR 14 [file glc.itp, line 1498]:
No default Proper Dih. types
Excluding 3 bonded neighbours molecule type ‘Other’
Excluding 3 bonded neighbours molecule type ‘GLC’
Excluding 2 bonded neighbours molecule type ‘SOL’
Removing all charge groups because cutoff-scheme=Verlet
There was 1 note
Program: gmx grompp, version 2016.4
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 1942)
Fatal error:
There were 14 errors in input file(s)
This file was generated by passing the glc.str file to the cgenff_charmm2gmx_py2.py . The glc.str file was generated by feeding the glc.mol2 file to the “https://cgenff.umaryland.edu/” ,But I checked the corresponding line in the glc.itp file and found that Dih. is not missing but complete.
I sincerely hope to receive your answers. Thank you
The conversion should have also generated a topology file that contains all the parameters needed by the molecule, with an extension .prm. You need to #include that in your system topology.
cause i cant upload the file; here is the [ dihedrals ] of glc.itp,the error line have been thickened.
; ai aj ak al funct c0 c1 c2 c3 c4 c5
12 1 2 3 9
12 1 2 13 9
12 1 2 7 9
135 1 2 3 9
135 1 2 13 9
135 1 2 7 9
10 1 2 3 9
10 1 2 13 9
10 1 2 7 9
2 1 135 130 9
12 1 135 130 9
10 1 135 130 9
2 1 10 5 9
12 1 10 5 9
135 1 10 5 9
1 2 3 4 9
1 2 3 14 9
1 2 3 8 9
13 2 3 4 9
13 2 3 14 9
13 2 3 8 9
7 2 3 4 9
7 2 3 14 9
7 2 3 8 9
1 2 7 19 9
3 2 7 19 9
13 2 7 19 9
2 3 4 9 9
2 3 4 5 9
2 3 4 15 9
14 3 4 9 9
14 3 4 5 9
14 3 4 15 9
8 3 4 9 9
8 3 4 5 9
8 3 4 15 9
2 3 8 20 9
4 3 8 20 9
14 3 8 20 9
3 4 9 22 9
5 4 9 22 9
15 4 9 22 9
9 4 5 10 9
9 4 5 6 9
9 4 5 16 9
3 4 5 10 9
3 4 5 6 9
3 4 5 16 9
15 4 5 10 9
15 4 5 6 9
15 4 5 16 9
4 5 10 1 9
6 5 10 1 9
16 5 10 1 9
10 5 6 17 9
10 5 6 18 9
10 5 6 11 9
4 5 6 17 9
4 5 6 18 9
4 5 6 11 9
16 5 6 17 9
16 5 6 18 9
16 5 6 11 9
17 6 11 21 9
18 6 11 21 9
5 6 11 21 9
4 9 22 33 9
4 9 22 31 9
4 9 22 23 9
33 22 31 26 9
9 22 31 26 9
23 22 31 26 9
33 22 23 34 9
33 22 23 28 9
33 22 23 24 9
9 22 23 34 9
9 22 23 28 9
9 22 23 24 9
31 22 23 34 9
31 22 23 28 9
31 22 23 24 9
34 23 28 40 9
22 23 28 40 9
24 23 28 40 9
34 23 24 25 9
34 23 24 35 9
34 23 24 29 9
28 23 24 25 9
28 23 24 35 9
28 23 24 29 9
22 23 24 25 9
22 23 24 35 9
22 23 24 29 9
35 24 25 26 9
35 24 25 36 9
35 24 25 30 9
29 24 25 26 9
29 24 25 36 9
29 24 25 30 9
23 24 25 26 9
23 24 25 36 9
23 24 25 30 9
25 24 29 41 9
35 24 29 41 9
23 24 29 41 9
36 25 26 27 9
36 25 26 37 9
36 25 26 31 9
30 25 26 27 9
30 25 26 37 9
30 25 26 31 9
24 25 26 27 9
24 25 26 37 9
24 25 26 31 9
26 25 30 43 9
36 25 30 43 9
24 25 30 43 9
25 26 27 38 9
25 26 27 39 9
25 26 27 32 9
37 26 27 38 9
37 26 27 39 9
37 26 27 32 9
31 26 27 38 9
31 26 27 39 9
31 26 27 32 9
25 26 31 22 9
27 26 31 22 9
37 26 31 22 9
26 27 32 42 9
38 27 32 42 9
39 27 32 42 9
25 30 43 44 9
25 30 43 52 9
25 30 43 54 9
52 43 44 49 9
52 43 44 45 9
52 43 44 55 9
30 43 44 49 9
30 43 44 45 9
30 43 44 55 9
54 43 44 49 9
54 43 44 45 9
54 43 44 55 9
44 43 52 47 9
30 43 52 47 9
54 43 52 47 9
43 44 49 61 9
45 44 49 61 9
55 44 49 61 9
49 44 45 50 9
49 44 45 46 9
49 44 45 56 9
43 44 45 50 9
43 44 45 46 9
43 44 45 56 9
55 44 45 50 9
55 44 45 46 9
55 44 45 56 9
44 45 50 62 9
46 45 50 62 9
56 45 50 62 9
50 45 46 57 9
50 45 46 51 9
50 45 46 47 9
44 45 46 57 9
44 45 46 51 9
44 45 46 47 9
56 45 46 57 9
56 45 46 51 9
56 45 46 47 9
57 46 51 64 9
45 46 51 64 9
47 46 51 64 9
57 46 47 58 9
57 46 47 52 9
57 46 47 48 9
51 46 47 58 9
51 46 47 52 9
51 46 47 48 9
45 46 47 58 9
45 46 47 52 9
45 46 47 48 9
58 47 52 43 9
46 47 52 43 9
48 47 52 43 9
58 47 48 59 9
58 47 48 60 9
58 47 48 53 9
52 47 48 59 9
52 47 48 60 9
52 47 48 53 9
46 47 48 59 9
46 47 48 60 9
46 47 48 53 9
59 48 53 63 9
60 48 53 63 9
47 48 53 63 9
46 51 64 73 9
46 51 64 65 9
46 51 64 75 9
65 64 73 68 9
51 64 73 68 9
75 64 73 68 9
73 64 65 66 9
73 64 65 76 9
73 64 65 70 9
51 64 65 66 9
51 64 65 76 9
51 64 65 70 9
75 64 65 66 9
75 64 65 76 9
75 64 65 70 9
76 65 66 67 9
76 65 66 77 9
76 65 66 71 9
70 65 66 67 9
70 65 66 77 9
70 65 66 71 9
64 65 66 67 9
64 65 66 77 9
64 65 66 71 9
66 65 70 82 9
76 65 70 82 9
64 65 70 82 9
65 66 67 68 9
65 66 67 78 9
65 66 67 72 9
77 66 67 68 9
77 66 67 78 9
77 66 67 72 9
71 66 67 68 9
71 66 67 78 9
71 66 67 72 9
65 66 71 83 9
67 66 71 83 9
77 66 71 83 9
66 67 68 73 9
66 67 68 69 9
66 67 68 79 9
78 67 68 73 9
78 67 68 69 9
78 67 68 79 9
72 67 68 73 9
72 67 68 69 9
72 67 68 79 9
66 67 72 85 9
68 67 72 85 9
78 67 72 85 9
67 68 73 64 9
69 68 73 64 9
79 68 73 64 9
73 68 69 81 9
73 68 69 74 9
73 68 69 80 9
67 68 69 81 9
67 68 69 74 9
67 68 69 80 9
79 68 69 81 9
79 68 69 74 9
79 68 69 80 9
81 69 74 84 9
68 69 74 84 9
80 69 74 84 9
67 72 85 96 9
67 72 85 86 9
67 72 85 94 9
96 85 86 97 9
96 85 86 91 9
96 85 86 87 9
94 85 86 97 9
94 85 86 91 9
94 85 86 87 9
72 85 86 97 9
72 85 86 91 9
72 85 86 87 9
96 85 94 89 9
86 85 94 89 9
72 85 94 89 9
97 86 91 103 9
85 86 91 103 9
87 86 91 103 9
97 86 87 98 9
97 86 87 92 9
97 86 87 88 9
91 86 87 98 9
91 86 87 92 9
91 86 87 88 9
85 86 87 98 9
85 86 87 92 9
85 86 87 88 9
98 87 92 104 9
86 87 92 104 9
88 87 92 104 9
98 87 88 89 9
98 87 88 99 9
98 87 88 93 9
92 87 88 89 9
92 87 88 99 9
92 87 88 93 9
86 87 88 89 9
86 87 88 99 9
86 87 88 93 9
99 88 89 90 9
99 88 89 100 9
99 88 89 94 9
93 88 89 90 9
93 88 89 100 9
93 88 89 94 9
87 88 89 90 9
87 88 89 100 9
87 88 89 94 9
89 88 93 106 9
99 88 93 106 9
87 88 93 106 9
100 89 90 101 9
100 89 90 102 9
100 89 90 95 9
94 89 90 101 9
94 89 90 102 9
94 89 90 95 9
88 89 90 101 9
88 89 90 102 9
88 89 90 95 9
90 89 94 85 9
100 89 94 85 9
88 89 94 85 9
89 90 95 105 9
101 90 95 105 9
102 90 95 105 9
88 93 106 117 9
88 93 106 107 9
88 93 106 115 9
117 106 107 108 9
117 106 107 118 9
117 106 107 112 9
93 106 107 108 9
93 106 107 118 9
93 106 107 112 9
115 106 107 108 9
115 106 107 118 9
115 106 107 112 9
117 106 115 110 9
107 106 115 110 9
93 106 115 110 9
106 107 108 113 9
106 107 108 109 9
106 107 108 119 9
118 107 108 113 9
118 107 108 109 9
118 107 108 119 9
112 107 108 113 9
112 107 108 109 9
112 107 108 119 9
106 107 112 124 9
108 107 112 124 9
118 107 112 124 9
107 108 113 125 9
109 108 113 125 9
119 108 113 125 9
113 108 109 114 9
113 108 109 110 9
113 108 109 120 9
107 108 109 114 9
107 108 109 110 9
107 108 109 120 9
119 108 109 114 9
119 108 109 110 9
119 108 109 120 9
108 109 114 127 9
110 109 114 127 9
120 109 114 127 9
114 109 110 121 9
114 109 110 115 9
114 109 110 111 9
108 109 110 121 9
108 109 110 115 9
108 109 110 111 9
120 109 110 121 9
120 109 110 115 9
120 109 110 111 9
121 110 115 106 9
109 110 115 106 9
111 110 115 106 9
121 110 111 122 9
121 110 111 123 9
121 110 111 116 9
115 110 111 122 9
115 110 111 123 9
115 110 111 116 9
109 110 111 122 9
109 110 111 123 9
109 110 111 116 9
122 111 116 126 9
123 111 116 126 9
110 111 116 126 9
109 114 127 138 9
109 114 127 136 9
109 114 127 128 9
138 127 136 131 9
114 127 136 131 9
128 127 136 131 9
138 127 128 129 9
138 127 128 139 9
138 127 128 133 9
136 127 128 129 9
136 127 128 139 9
136 127 128 133 9
114 127 128 129 9
114 127 128 139 9
114 127 128 133 9
139 128 129 130 9
139 128 129 140 9
139 128 129 134 9
133 128 129 130 9
133 128 129 140 9
133 128 129 134 9
127 128 129 130 9
127 128 129 140 9
127 128 129 134 9
129 128 133 145 9
139 128 133 145 9
127 128 133 145 9
140 129 130 131 9
140 129 130 141 9
140 129 130 135 9
134 129 130 131 9
134 129 130 141 9
134 129 130 135 9
128 129 130 131 9
128 129 130 141 9
128 129 130 135 9
130 129 134 146 9
140 129 134 146 9
128 129 134 146 9
129 130 131 132 9
129 130 131 142 9
129 130 131 136 9
141 130 131 132 9
141 130 131 142 9
141 130 131 136 9
135 130 131 132 9
135 130 131 142 9
135 130 131 136 9
129 130 135 1 9
131 130 135 1 9
141 130 135 1 9
130 131 132 137 9
130 131 132 143 9
130 131 132 144 9
142 131 132 137 9
142 131 132 143 9
142 131 132 144 9
136 131 132 137 9
136 131 132 143 9
136 131 132 144 9
130 131 136 127 9
132 131 136 127 9
142 131 136 127 9
131 132 137 147 9
143 132 137 147 9
144 132 137 147 9
Thank you very much for your reply! But I have put files with the .prm extension in my top file.It didn’t work.
Sorry but “it didn’t work” isn’t helpful. Did you get an error? Is the #include statement in the proper location (it has specific syntactical requirements)? The protocol is explained in detail in this tutorial: Protein-Ligand Complex
I have followed the tutorial strictly,my ligand glc.pdb was added with hydrogen ions to get mol2 file, and then it was converted into str file on cgenff website. The subsequent steps were consistent with the tutorial, but 14 errors popped up in the process of energy minimization.
Are you using the March 2019 version of the CHARMM port as in the tutorial, or the July 2022 (latest release)? If you aren’t using the latest, do so and see if that fixes the issue.
Thank you so much, that’s exactly the reason for the mistake. Your answer is very valuable！