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jackeychen04

木虫 (小有名气)

应助: 7 (幼儿园)
金币: 2947.2
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在线: 103.5小时
虫号: 881896
注册: 2009-10-23
专业: 天然药物化学

[求助] 分子对接中mol文件用open babel 转化为mol2

因课题需要本人刚接触分子对接，不是很熟悉这个，看文献先画出分子平面结构，然后我是在在线将平面结构转化为3D结构http://davapc1.bioch.dundee.ac.uk/prodrg/index.html
最后用open babel 加氢加电贺，这个不知到具体步骤
想问问各位大侠。
我最终想要得到如下格式的mol2文件
@MOLECULE
HUP999
37 39    1    0    4
SMALL
GASTEIGER

@DICT
SMALL
@ATOM
   1 H1       2.9427 68.8027 60.0338 H       1 HUP999    0.1548
   2 H2       -0.7396 69.1138 62.0324 H       1 HUP999    0.0669
   3 H3       0.3492 68.3943 64.0675 H       1 HUP999    0.0624
   4 H4       5.0199 69.1085 61.7835 H       1 HUP999    0.0334
   5 H5       4.7500 67.4801 61.0750 H       1 HUP999    0.0334
   6 H6       6.1947 67.5970 63.2325 H       1 HUP999    0.0394
   7 H7       5.4043 65.3009 62.7546 H       1 HUP999    0.0578
   8 H8       6.5925 70.6254 65.4723 H       1 HUP999    0.0272
   9 H9       6.6645 69.9561 63.8069 H       1 HUP999    0.0272
   10 H10       7.1342 68.9334 65.2070 H       1 HUP999    0.0272
   11 H11       4.3916 69.8366 65.6345 H       1 HUP999    0.0571
   12 H12       1.4640 68.3437 65.7702 H       1 HUP999    0.2006
   13 H13       2.5059 69.5948 65.5282 H       1 HUP999    0.2006
   14 H14       2.9113 68.3726 66.5536 H       1 HUP999    0.2006
   15 H15       1.8746 66.0893 64.6984 H       1 HUP999    0.0375
   16 H16       3.1615 66.2279 65.9441 H       1 HUP999    0.0375
   17 H17       4.2285 63.4492 63.6170 H       1 HUP999    0.0274
   18 H18       2.4999 63.7965 63.9603 H       1 HUP999    0.0274
   19 C1       1.0705 69.0592 60.8048 C.2    1 HUP999    0.2409
   20 O1       0.5652 69.4351 59.7182 O.2    1 HUP999    -0.2705
   21 N1       2.4050 68.7393 60.8745 N.am    1 HUP999    -0.2851
   22 C2       0.3295 68.9066 62.0228 C.2    1 HUP999    0.0010
   23 C3       0.9458 68.5069 63.1635 C.2    1 HUP999    -0.0462
   24 C4       2.3432 68.2281 63.2271 C.2    1 HUP999    0.0250
   25 C5       3.0634 68.3317 62.0372 C.2    1 HUP999    0.0207
   26 C6       4.5347 68.1328 61.9338 C.3    1 HUP999    -0.0038
   27 C7       5.1014 67.4763 63.2267 C.3    1 HUP999    0.0094
   28 C8       4.7896 65.9969 63.3235 C.2    1 HUP999    -0.0771
   29 C9       6.4506 69.7224 64.8603 C.3    1 HUP999    -0.0463
   30 C10       5.0453 69.2524 64.9885 C.2    1 HUP999    -0.0814
   31 C11       4.5150 68.2109 64.4057 C.2    1 HUP999    -0.0112
   32 C12       3.0565 67.8689 64.5747 C.3    1 HUP999    0.0397
   33 N2       2.4351 68.6033 65.6957 N.4    1 HUP999    0.2297
   34 C13       2.9186 66.3830 64.8825 C.3    1 HUP999    0.0225
   35 C14       3.7982 65.5024 64.0718 C.2    1 HUP999    -0.0697
   36 C15       3.5364 64.0232 64.2506 C.3    1 HUP999    -0.0435
   37 H19       3.6905 63.7483 65.3045 H       1 HUP999    0.0274
@BOND
   1 21 1 1
   2 22 2 1
   3 23 3 1
   4 26 4 1
   5 26 5 1
   6 27 6 1
   7 28 7 1
   8 29 8 1
   9 29 9 1
10 29 10 1
11 30 11 1
12 33 12 1
13 33 13 1
14 33 14 1
15 34 15 1
16 34 16 1
17 36 17 1
18 36 18 1
19 19 20 2
20 21 19 am
21 22 19 1
22 25 21 am
23 23 22 2
24 24 23 1
25 24 25 2
26 32 24 1
27 26 25 1
28 27 26 1
29 28 27 1
30 27 31 1
31 35 28 2
32 30 29 1
33 31 30 2
34 32 31 1
35 32 33 1
36 34 32 1
37 35 34 1
38 35 36 1
39 36 37 1
@SUBSTRUCTURE
   1 HUP999    19 GROUP          0 A    **** 0 ROOT
@SET
UNK_ATOMS    STATIC    ATOMS AMSOM **** Atom types guessed for these atoms
18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36
LAB$A_USER    STATIC    ATOMS LABELGROUP SYSTEM
18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36
LAB$A_TYPE    STATIC    ATOMS LABELGROUP SYSTEM
18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36
ATOM$INVISIBLE  STATIC    ATOMS DISPGROUP SYSTEM
0

但是我现在的文件（具体见附件Jun927562.rar）
dava@davapc1.bioch.dundee.ac.uk
REMARK
REMARK  When using this software in a publication, cite:
REMARK  A. W. Schuettelkopf and D. M. F. van Aalten (2004).
REMARK  PRODRG - a tool for high-throughput crystallography
REMARK  of protein-ligand complexes.
REMARK  Acta Crystallogr. D60, 1355--1363.
REMARK
REMARK
HETATM 1  CAD DRG    1    2.420  -7.230 1.180  1.00 20.00          C
HETATM 2 1HAD DRG    1    2.851  -7.280 2.081  1.00 20.00          H
HETATM 3 2HAD DRG    1    2.982  -7.720 0.514  1.00 20.00          H
HETATM 4  NAE DRG    1    2.150  -5.850 0.770  1.00 20.00          N
HETATM 5  HAA DRG    1    2.810  -5.290 0.280  1.00 20.00          H
HETATM 6  CAG DRG    1    0.910  -5.550 1.170  1.00 20.00          C
HETATM 7  SAB DRG    1    0.150  -4.040 0.900  1.00 20.00          S
HETATM 8  OAF DRG    1    0.330  -6.600 1.810  1.00 20.00          O
HETATM 9  CAH DRG    1    0.980  -7.730 1.200  1.00 20.00          C
HETATM 10 1HAH DRG    1    0.596  -7.992 0.315  1.00 20.00          H
HETATM 11  CAC DRG    1    0.880  -8.880 1.980  1.00 20.00          C
HETATM 12 1HAC DRG    1    1.694  -9.237 2.439  1.00 20.00          H
HETATM 13  CAA DRG    1    -0.340  -9.540 2.130  1.00 20.00          C
HETATM 14 1HAA DRG    1    -0.397 -10.364 2.693  1.00 20.00          H
HETATM 15 2HAA DRG    1    -1.158  -9.189 1.674  1.00 20.00          H
CONECT 1 2 3 4 9
CONECT 2 1
CONECT 3 1
CONECT 4 1 5 6
CONECT 5 4
CONECT 6 4 7 8
CONECT 7 6
CONECT 8 6 9
CONECT 9 1 8 10 11
CONECT 10 9
CONECT 11 9 12 13
CONECT 12 11
CONECT 13 11 14 15
CONECT 14 13
CONECT 15 13
END

如何用open babel 转化成上面格式的mol2文件格式呢，如果open babel不行，该怎么转

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