OpenBabel中的obminimize使用问题

清少纳华 发表于 2013-1-7 21:20:05

本人使用命令 obminimize -ff MMFF94 -n 300 filename.mol2 对mol2格式的分子进行能量优化，运行正常，但不知道优化完结果是不是覆盖优化前的源文件，于是查看源文件发现源文件创建时间和修改时间都没变，于是我又将运行结果写到新的文件KZI.mol2，打开得到下面的结果：
COMPND KZI
AUTHOR GENERATED BY OPEN BABEL 2.3.0
ATOM    1O LIG A 1    1.816-4.281 0.0601.000.00       O
ATOM    2O LIG A 1    1.765 3.142 0.9831.000.00       O
ATOM    3O LIG A 1    5.654 0.737-0.8151.000.00       O
ATOM    4N LIG A 1    -0.595-0.785 0.2731.000.00       N
ATOM    5N LIG A 1    -2.664 0.150 0.2951.000.00       N
ATOM    6N LIG A 1    -0.066-5.523-0.1821.000.00       N
ATOM    7N LIG A 1    -1.626-3.376-0.0231.000.00       N
ATOM    8N LIG A 1    1.649-1.594 0.2671.000.00       N
ATOM    9C LIG A 1    3.781 2.060 0.0741.000.00       C
ATOM 10C LIG A 1    -4.403 0.330-1.4341.000.00       C
ATOM 11C LIG A 1    3.675-0.344-0.2061.000.00       C
ATOM 12C LIG A 1    0.260-1.836 0.2141.000.00       C
ATOM 13C LIG A 1    0.592-4.333-0.0101.000.00       C
ATOM 14C LIG A 1    -2.413-2.275 0.0411.000.00       C
ATOM 15C LIG A 1    1.792 0.838 0.6771.000.00       C
ATOM 16C LIG A 1    -0.281-3.123 0.0741.000.00       C
ATOM 17C LIG A 1    2.361-0.378 0.2801.000.00       C
ATOM 18C LIG A 1    2.480 2.050 0.5711.000.00       C
ATOM 19C LIG A 1    -4.087 0.331 0.0681.000.00       C
ATOM 20C LIG A 1    2.358 4.418 0.7941.000.00       C
ATOM 21C LIG A 1    -1.923-0.986 0.1971.000.00       C
ATOM 22C LIG A 1    4.385 0.861-0.3111.000.00       C
ATOM 23C LIG A 1    -4.575 1.656 0.7421.000.00       C
ATOM 24C LIG A 1    -3.914 1.589-2.1481.000.00       C
ATOM 25C LIG A 1    -4.465 2.850-1.4931.000.00       C
ATOM 26C LIG A 1    6.405 1.935-0.9691.000.00       C
ATOM 27C LIG A 1    -4.111 2.911-0.0121.000.00       C
ATOM 28N LIG A 1    -4.133 1.777 2.1391.000.00       N
ATOM 29H LIG A 1    -2.100 0.980 0.4531.000.00       H
ATOM 30H LIG A 1    0.455-6.385-0.2501.000.00       H
ATOM 31H LIG A 1    -1.079-5.527-0.2511.000.00       H
ATOM 32H LIG A 1    2.215-2.435 0.1391.000.00       H
ATOM 33H LIG A 1    4.317 2.994-0.0101.000.00       H
ATOM 34H LIG A 1    -3.969-0.550-1.9231.000.00       H
ATOM 35H LIG A 1    -5.490 0.254-1.5631.000.00       H
ATOM 36H LIG A 1    4.156-1.262-0.5351.000.00       H
ATOM 37H LIG A 1    -3.476-2.469-0.0271.000.00       H
ATOM 38H LIG A 1    0.788 0.869 1.0881.000.00       H
ATOM 39H LIG A 1    -4.627-0.497 0.5451.000.00       H
ATOM 40H LIG A 1    3.257 4.527 1.4101.000.00       H
ATOM 41H LIG A 1    2.577 4.602-0.2631.000.00       H
ATOM 42H LIG A 1    1.637 5.174 1.1201.000.00       H
ATOM 43H LIG A 1    -5.673 1.639 0.7371.000.00       H
ATOM 44H LIG A 1    -2.818 1.619-2.1441.000.00       H
ATOM 45H LIG A 1    -4.226 1.557-3.1981.000.00       H
ATOM 46H LIG A 1    -4.066 3.734-2.0031.000.00       H
ATOM 47H LIG A 1    -5.555 2.879-1.6101.000.00       H
ATOM 48H LIG A 1    5.924 2.613-1.6831.000.00       H
ATOM 49H LIG A 1    6.567 2.428-0.0041.000.00       H
ATOM 50H LIG A 1    7.386 1.668-1.3731.000.00       H
ATOM 51H LIG A 1    -4.572 3.805 0.4281.000.00       H
ATOM 52H LIG A 1    -3.025 3.040 0.0891.000.00       H
ATOM 53H LIG A 1    -4.652 2.514 2.6131.000.00       H
ATOM 54H LIG A 1    -4.304 0.907 2.6401.000.00       H
CONECT 1 13
CONECT 2 18 20
CONECT 3 22 26
CONECT 4 12 21
CONECT 5 19 21 29
CONECT 6 13 30 31
CONECT 7 14 16
CONECT 8 12 17 32
CONECT 9 18 22 33
CONECT 10 19 24 34 35
CONECT 10
CONECT 11 17 22 36
CONECT 12 4 8 16
CONECT 13 1 6 16
CONECT 14 7 21 37
CONECT 15 17 18 38
CONECT 16 7 12 13
CONECT 17 8 11 15
CONECT 18 2 9 15
CONECT 19 5 10 23 39
CONECT 19
CONECT 20 2 40 41 42
CONECT 20
CONECT 21 4 5 14
CONECT 22 3 9 11
CONECT 23 19 27 28 43
CONECT 23
CONECT 24 10 25 44 45
CONECT 24
CONECT 25 24 27 46 47
CONECT 25
CONECT 26 3 48 49 50
CONECT 26
CONECT 27 23 25 51 52
CONECT 27
CONECT 28 23 53 54
CONECT 29 5
CONECT 30 6
CONECT 31 6
CONECT 32 8
CONECT 33 9
CONECT 34 10
CONECT 35 10
CONECT 36 11
CONECT 37 14
CONECT 38 15
CONECT 39 19
CONECT 40 20
CONECT 41 20
CONECT 42 20
CONECT 43 23
CONECT 44 24
CONECT 45 24
CONECT 46 25
CONECT 47 25
CONECT 48 26
CONECT 49 26
CONECT 50 26
CONECT 51 27
CONECT 52 27
CONECT 53 28
CONECT 54 28
MASTER    0 0 0 0 0 0 0 0 54 0 54 0
END

但这明显不是mol2格式的文件，请问大神到底如何得到obminimize优化后的mol2文件？

eming 发表于 2013-1-8 00:11:38

再用babel转一下就ok了

清少纳华 发表于 2013-1-8 13:37:08

eming 发表于 2013-1-8 00:11 static/image/common/back.gif
再用babel转一下就ok了

再用 babel -imol2 KZI.mol2 -omol2 out.mol2 转换吗？我试过的，转换不了，因为它本身不是mol2文件格式，babel识别不了它。

eming 发表于 2013-1-10 17:13:04

清少纳华发表于 2013-1-8 13:37 static/image/common/back.gif
再用 babel -imol2 KZI.mol2 -omol2 out.mol2 转换吗？我试过的，转换不了，因为它本身不是mol2文件格式 ...

既然是pdb的，为啥imol2啊

清少纳华 发表于 2013-1-11 14:58:29

eming 发表于 2013-1-10 17:13 static/image/common/back.gif
既然是pdb的，为啥imol2啊

= =一直不知道，原来obminimize的结果是pdb格式啊，看来要优化一下还挺复杂的，转来转去的。谢谢你eming ！

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OpenBabel中的obminimize使用问题