[gmx-users] Fwd:
RAHUL SURESH
drrahulsuresh at gmail.com
Wed Apr 12 21:15:28 CEST 2017
I wish to do dynamic study on interation of porphyine with graphene and
when I tried to covert below .mol2 file using cGenff
@<TRIPOS>MOLECULE
E:\research\porphyrine\grper.log
83 99 0 0 0
SMALL
MULLIKEN_CHARGES
****
Gaussian 09 #PBE1PBE/cc-pVDZ opt freq
@<TRIPOS>ATOM
1 C 1.3473 -0.6473 -1.2468 Car 1 LIG1 0.1043
2 C 2.5156 -1.4011 -0.9462 Car 1 LIG1 0.0435
3 C 3.7307 -0.7368 -0.6479 Car 1 LIG1 0.0819
4 C 1.3916 0.7696 -1.2149 Car 1 LIG1 0.0928
5 C 3.7772 0.6843 -0.6218 Car 1 LIG1 0.0815
6 C 4.9018 -1.4913 -0.3733 Car 1 LIG1 -0.0733
7 C 3.6499 -3.5571 -0.6690 Car 1 LIG1 0.0219
8 C 4.8291 -2.9092 -0.3876 Car 1 LIG1 0.0323
9 H 5.7321 -3.4860 -0.1784 1 1 LIG1 0.0362
10 C 2.6061 1.4359 -0.8883 Car 1 LIG1 0.0441
11 C 0.2291 1.5214 -1.5218 Car 1 LIG1 0.0742
12 C 2.6464 2.8586 -0.8462 Car 1 LIG1 -0.0384
13 C 0.2700 2.9434 -1.4708 Car 1 LIG1 -0.0447
14 C 1.4714 3.5825 -1.1209 Car 1 LIG1 0.0139
15 H 1.5023 4.6748 -1.0919 1 1 LIG1 0.0203
16 C 2.4651 -2.8238 -0.9643 Car 1 LIG1 -0.0309
17 C -0.9682 0.8605 -1.8936 Car 1 LIG1 0.0143
18 H 3.6162 -4.6485 -0.6855 1 1 LIG1 0.0307
19 C -2.1217 1.6178 -2.2579 Car 1 LIG1 -0.0393
20 C -2.0585 3.0309 -2.1934 Car 1 LIG1 0.0308
21 C -0.9063 3.6752 -1.7987 Car 1 LIG1 0.0395
22 H -2.9384 3.6127 -2.4745 1 1 LIG1 0.0272
23 H -0.8758 4.7661 -1.7638 1 1 LIG1 0.0292
24 C 0.1011 -2.7329 -1.6400 Car 1 LIG1 -0.0368
25 C -2.1950 -1.2222 -2.3715 Car 1 LIG1 -0.0380
26 C 0.1436 -1.3109 -1.6000 Car 1 LIG1 0.0418
27 C 1.2533 -3.4604 -1.2937 Car 1 LIG1 0.0033
28 H -1.1293 -4.4626 -2.1072 1 1 LIG1 0.0274
29 C -1.0089 -0.5585 -1.9432 Car 1 LIG1 0.0179
30 C -3.2894 0.9300 -2.6922 Car 1 LIG1 0.0371
31 H -4.1602 1.5133 -2.9967 1 1 LIG1 0.0257
32 H 1.2202 -4.5528 -1.3250 1 1 LIG1 0.0187
33 C 6.1610 0.5705 -0.0653 Car 1 LIG1 0.0354
34 C 6.1160 -0.7980 -0.0882 Car 1 LIG1 0.0361
35 H 7.0996 1.0838 0.1526 1 1 LIG1 0.0361
36 H 7.0187 -1.3786 0.1117 1 1 LIG1 0.0359
37 C 4.9946 1.3511 -0.3240 Car 1 LIG1 -0.0769
38 C 5.0147 2.7712 -0.2881 Car 1 LIG1 0.0338
39 C 3.8789 3.5033 -0.5358 Car 1 LIG1 0.0220
40 H 5.9540 3.2801 -0.0634 1 1 LIG1 0.0364
41 H 3.9144 4.5944 -0.5096 1 1 LIG1 0.0313
42 C -2.2049 -2.6385 -2.4246 Car 1 LIG1 0.0301
43 C -1.1007 -3.3725 -2.0579 Car 1 LIG1 0.0437
44 H -3.1074 -3.1476 -2.7681 1 1 LIG1 0.0254
45 C -3.3243 -0.4399 -2.7492 Car 1 LIG1 0.0275
46 H -4.2212 -0.9504 -3.1053 1 1 LIG1 0.0248
47 N -3.3826 0.2886 0.7750 Nar 2 LIG2 -0.4457
48 N -1.1998 1.8969 1.5415 Nar 2 LIG2 -0.4503
49 N -1.8402 -2.0337 1.2307 Nar 2 LIG2 -0.4495
50 N 0.3385 -0.4260 2.0012 Nar 2 LIG2 -0.4540
51 C -4.0027 1.5228 0.6502 Car 2 LIG2 0.1780
52 C -2.0828 2.9051 1.3269 Car 2 LIG2 0.1758
53 C -4.3356 -0.6178 0.4561 Car 2 LIG2 0.1754
54 C -0.0405 2.5206 1.9661 Car 2 LIG2 0.1802
55 C -3.4157 2.7344 0.9082 C2 2 LIG2 -0.0337
56 C -5.3828 1.3553 0.2372 Car 2 LIG2 0.0212
57 C -1.4968 4.1955 1.6113 Car 2 LIG2 0.0046
58 C -5.5897 0.0234 0.1166 Car 2 LIG2 0.0118
59 C -0.2211 3.9572 2.0040 Car 2 LIG2 0.0122
60 C -4.1674 -2.0160 0.4788 C2 2 LIG2 -0.0382
61 C 1.1123 1.8749 2.3413 C2 2 LIG2 -0.0333
62 C -3.0140 -2.6589 0.8466 Car 2 LIG2 0.1817
63 C 1.2797 0.4822 2.3640 Car 2 LIG2 0.1763
64 C -0.9916 -3.0431 1.5473 Car 2 LIG2 0.1826
65 C 0.9270 -1.6585 2.2183 Car 2 LIG2 0.1794
66 C 0.3256 -2.8746 2.0063 C2 2 LIG2 -0.0429
67 C -2.8693 -4.1004 0.9224 Car 2 LIG2 0.0213
68 C 2.4925 -0.1641 2.8167 Car 2 LIG2 0.0103
69 C -1.6114 -4.3373 1.3663 Car 2 LIG2 0.0043
70 C 2.2720 -1.4977 2.7286 Car 2 LIG2 0.0206
71 H -4.0245 3.6319 0.7932 1 2 LIG2 0.0293
72 H -6.0893 2.1691 0.0860 1 2 LIG2 0.0393
73 H -2.0193 5.1468 1.5351 1 2 LIG2 0.0338
74 H -6.5029 -0.5006 -0.1577 1 2 LIG2 0.0373
75 H 0.5346 4.6697 2.3284 1 2 LIG2 0.0323
76 H -5.0303 -2.6276 0.2124 1 2 LIG2 0.0304
77 H 1.9534 2.4855 2.6717 1 2 LIG2 0.0242
78 H 0.8951 -3.7742 2.2422 1 2 LIG2 0.0250
79 H -3.6545 -4.8165 0.6883 1 2 LIG2 0.0391
80 H 3.3792 0.3567 3.1714 1 2 LIG2 0.0290
81 H -1.1338 -5.2922 1.5758 1 2 LIG2 0.0329
82 H 2.9371 -2.3168 2.9934 1 2 LIG2 0.0307
83 FE -1.5118 -0.0678 1.3527 26 2 LIG2 0.9981
@<TRIPOS>BOND
1 46 45 1
2 31 30 1
3 44 42 1
4 45 30 ar
5 45 25 ar
6 30 19 ar
7 22 20 1
8 42 25 ar
9 42 43 ar
10 25 29 ar
11 19 20 ar
12 19 17 ar
13 20 21 ar
14 28 43 1
15 43 24 ar
16 29 17 ar
17 29 26 ar
18 17 11 ar
19 21 23 1
20 21 13 ar
21 24 26 ar
22 24 27 ar
23 26 1 ar
24 11 13 ar
25 11 4 ar
26 13 14 ar
27 32 27 1
28 27 16 ar
29 1 4 ar
30 1 2 ar
31 4 10 ar
32 14 15 1
33 14 12 ar
34 16 2 ar
35 16 7 ar
36 2 3 ar
37 10 12 ar
38 10 5 ar
39 12 39 ar
40 18 7 1
41 7 8 ar
42 3 5 ar
43 3 6 ar
44 5 37 ar
45 39 41 1
46 39 38 ar
47 8 6 ar
48 8 9 1
49 6 34 ar
50 37 38 ar
51 37 33 ar
52 38 40 1
53 74 58 1
54 34 33 ar
55 34 36 1
56 33 35 1
57 72 56 1
58 58 56 ar
59 58 53 ar
60 76 60 1
61 56 51 ar
62 53 60 2
63 53 47 ar
64 60 62 1
65 51 47 ar
66 51 55 2
67 79 67 1
68 47 83 1
69 71 55 1
70 62 67 ar
71 62 49 ar
72 55 52 1
73 67 69 ar
74 49 83 1
75 49 64 ar
76 52 48 ar
77 52 57 ar
78 83 48 1
79 83 50 1
80 69 64 ar
81 69 81 1
82 73 57 1
83 48 54 ar
84 64 66 2
85 57 59 ar
86 54 59 ar
87 54 61 2
88 50 65 ar
89 50 63 ar
90 59 75 1
91 66 65 1
92 66 78 1
93 65 70 ar
94 61 63 1
95 61 77 1
96 63 68 ar
97 70 68 ar
98 70 82 1
99 68 80 1
I obtain following error:
readmol2 warning: non-unique atoms were renamed.
Now processing molecule grper ...
attype warning: element not supported;
skipped molecule.
kindly help me to solve this issue.
--
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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