小分子能量最小化
系列：
处理小分子
目的：
小分子能量最小化
原理：
Pymol创建小分子+Openbabel进行最小化
步骤：
（1）PyMol创建小分子，然后保存为mol2格式
（2）运行openbabel进行能量最小化处理
指令：obminimize test.mol2
输入参数：
-n steps
Specify the maximum number of steps (default=2500)
-cg
Use conjugate gradients algorithm (default)
-sd
Use steepest descent algorithm
-c criteria
Set convergence criteria (default=1e-6)
-ff forcefield
Select the forcefield
（3）最终输出结果需要手动保存为pdb格式
COMPND obj06
AUTHOR GENERATED BY OPEN BABEL 2.4.1
ATOM 1 C01 UNK A 1 -1.328 0.979 -0.999 1.00 0.00 C
ATOM 2 C07 UNK A 1 -3.145 -0.704 -1.089 1.00 0.00 C
ATOM 3 C09 UNK A 1 -5.040 -2.344 -1.150 1.00 0.00 C
ATOM 4 C11 UNK A 1 -7.274 -3.408 -1.751 1.00 0.00 C
ATOM 5 C13 UNK A 1 -3.816 -4.091 0.196 1.00 0.00 C
ATOM 6 C15 UNK A 1 -2.840 -5.211 0.139 1.00 0.00 C
ATOM 7 C21 UNK A 1 -4.413 -3.623 1.469 1.00 0.00 C
ATOM 8 C27 UNK A 1 3.812 1.596 -0.512 1.00 0.00 C
ATOM 9 C29 UNK A 1 -9.369 -3.106 -0.413 1.00 0.00 C
ATOM 10 C31 UNK A 1 -7.134 -5.548 -2.998 1.00 0.00 C
ATOM 11 C02 UNK A 1 -0.427 0.342 -0.138 1.00 0.00 C
ATOM 12 C08 UNK A 1 -2.738 0.575 -1.092 1.00 0.00 C
ATOM 13 C10 UNK A 1 -4.544 -1.084 -1.165 1.00 0.00 C
ATOM 14 C12 UNK A 1 -6.503 -2.485 -1.127 1.00 0.00 C
ATOM 15 C14 UNK A 1 -4.142 -3.487 -0.970 1.00 0.00 C
ATOM 16 C16 UNK A 1 -1.589 -5.057 -0.478 1.00 0.00 C
ATOM 17 C22 UNK A 1 -5.703 -4.020 1.847 1.00 0.00 C
ATOM 18 C28 UNK A 1 2.732 2.357 -0.731 1.00 0.00 C
ATOM 19 C30 UNK A 1 -8.730 -3.343 -1.567 1.00 0.00 C
ATOM 20 C32 UNK A 1 -6.693 -4.308 -2.748 1.00 0.00 C
ATOM 21 C03 UNK A 1 0.902 0.774 -0.049 1.00 0.00 C
ATOM 22 C17 UNK A 1 -0.675 -6.112 -0.508 1.00 0.00 C
ATOM 23 C23 UNK A 1 -6.253 -3.575 3.050 1.00 0.00 C
ATOM 24 C04 UNK A 1 1.356 1.851 -0.818 1.00 0.00 C
ATOM 25 C18 UNK A 1 -0.996 -7.330 0.087 1.00 0.00 C
ATOM 26 C24 UNK A 1 -5.517 -2.734 3.884 1.00 0.00 C
ATOM 27 C05 UNK A 1 0.445 2.507 -1.655 1.00 0.00 C
ATOM 28 C19 UNK A 1 -2.230 -7.493 0.714 1.00 0.00 C
ATOM 29 C25 UNK A 1 -4.231 -2.338 3.518 1.00 0.00 C
ATOM 30 C06 UNK A 1 -0.884 2.075 -1.744 1.00 0.00 C
ATOM 31 C20 UNK A 1 -3.145 -6.438 0.743 1.00 0.00 C
ATOM 32 C26 UNK A 1 -3.679 -2.783 2.315 1.00 0.00 C
ATOM 33 H01 UNK A 1 -2.411 -1.503 -1.027 1.00 0.00 H
ATOM 34 H32 UNK A 1 4.800 2.044 -0.470 1.00 0.00 H
ATOM 35 H35 UNK A 1 -10.454 -3.096 -0.379 1.00 0.00 H
ATOM 36 H38 UNK A 1 -6.652 -6.162 -3.752 1.00 0.00 H
ATOM 37 H33 UNK A 1 3.753 0.520 -0.386 1.00 0.00 H
ATOM 38 H36 UNK A 1 -8.840 -2.933 0.518 1.00 0.00 H
ATOM 39 H39 UNK A 1 -7.966 -5.984 -2.454 1.00 0.00 H
ATOM 40 H04 UNK A 1 -3.456 1.387 -1.178 1.00 0.00 H
ATOM 41 H15 UNK A 1 -5.243 -0.251 -1.237 1.00 0.00 H
ATOM 42 H17 UNK A 1 -6.987 -1.749 -0.484 1.00 0.00 H
ATOM 43 H20 UNK A 1 -3.709 -3.842 -1.904 1.00 0.00 H
ATOM 44 H34 UNK A 1 2.860 3.428 -0.878 1.00 0.00 H
ATOM 45 H37 UNK A 1 -9.321 -3.545 -2.459 1.00 0.00 H
ATOM 46 H40 UNK A 1 -5.846 -3.933 -3.319 1.00 0.00 H
ATOM 47 H08 UNK A 1 -0.750 -0.486 0.488 1.00 0.00 H
ATOM 48 H21 UNK A 1 -1.313 -4.109 -0.934 1.00 0.00 H
ATOM 49 H27 UNK A 1 -6.283 -4.673 1.199 1.00 0.00 H
ATOM 50 H09 UNK A 1 1.569 0.267 0.644 1.00 0.00 H
ATOM 51 H22 UNK A 1 0.290 -5.981 -0.991 1.00 0.00 H
ATOM 52 H28 UNK A 1 -7.255 -3.885 3.335 1.00 0.00 H
ATOM 53 H23 UNK A 1 -0.284 -8.151 0.066 1.00 0.00 H
ATOM 54 H29 UNK A 1 -5.946 -2.388 4.821 1.00 0.00 H
ATOM 55 H11 UNK A 1 0.761 3.358 -2.253 1.00 0.00 H
ATOM 56 H24 UNK A 1 -2.481 -8.441 1.183 1.00 0.00 H
ATOM 57 H30 UNK A 1 -3.657 -1.683 4.168 1.00 0.00 H
ATOM 58 H12 UNK A 1 -1.564 2.602 -2.409 1.00 0.00 H
ATOM 59 H25 UNK A 1 -4.102 -6.585 1.238 1.00 0.00 H
ATOM 60 H31 UNK A 1 -2.677 -2.468 2.037 1.00 0.00 H
CONECT 1 11 12 30
CONECT 2 12 13 33
CONECT 3 13 14 15
CONECT 4 14 19 20
CONECT 5 6 7 15
CONECT 6 5 16 31
CONECT 7 5 17 32
CONECT 8 18 34 37
CONECT 9 19 35 38
CONECT 10 20 36 39
CONECT 11 1 21 47
CONECT 12 1 2 40
CONECT 13 2 3 41
CONECT 14 3 4 42
CONECT 15 3 5 43
CONECT 16 6 22 48
CONECT 17 7 23 49
CONECT 18 8 44 24
CONECT 19 4 9 45
CONECT 20 4 10 46
CONECT 21 11 24 50
CONECT 22 16 25 51
CONECT 23 17 26 52
CONECT 24 21 18 27
CONECT 25 22 28 53
CONECT 26 23 29 54
CONECT 27 24 30 55
CONECT 28 25 31 56
CONECT 29 26 32 57
CONECT 30 1 27 58
CONECT 31 6 28 59
CONECT 32 7 29 60
CONECT 33 2
CONECT 34 8
CONECT 35 9
CONECT 36 10
CONECT 37 8
CONECT 38 9
CONECT 39 10
CONECT 40 12
CONECT 41 13
CONECT 42 14
CONECT 43 15
CONECT 44 18
CONECT 45 19
CONECT 46 20
CONECT 47 11
CONECT 48 16
CONECT 49 17
CONECT 50 21
CONECT 51 22
CONECT 52 23
CONECT 53 25
CONECT 54 26
CONECT 55 27
CONECT 56 28
CONECT 57 29
CONECT 58 30
CONECT 59 31
CONECT 60 32
MASTER 0 0 0 0 0 0 0 0 60 0 60 0
END输出：
Everyday you must keep something new.
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原始发表：2020-07-29，如有侵权请联系 cloudcommunity@tencent.com 删除
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