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xixi1007

木虫 (小有名气)

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虫号: 571532
注册: 2008-06-10

[求助] 求助amber的pdb格式

最近刚开始学习amber,但自建分子的pdb格式老是不对，还请各位帮忙看一下，应该怎么设置pdb格式。下面是我的一个例子ACE-GLY-ALA-GLY-NME。给出的是用hyperchem构建的pdb。适合amber格式的pdb应该是什么样的呢。请给位高手给一个准确的pdb格式。谢谢了！
ATOM    1 1H ACE    1    0.022 0.000  -0.001
ATOM    2  CH3 ACE    1    0.022 1.090  -0.001
ATOM    3 2H ACE    1    1.049 1.453 0.006
ATOM    4 3H ACE    1    -0.486 1.453  -0.894
ATOM    5  C ACE    1    -0.708 1.600 1.244
ATOM    6  O ACE    1    -0.827 2.806 1.447
ATOM    7  N GLY    2    -1.219 0.728 2.116
ATOM    8  H GLY    2    -1.115  -0.261 1.939
ATOM    9  CA  GLY    2    -1.919 1.159 3.309
ATOM    10 1HA  GLY    2    -2.810 1.719 3.026
ATOM    11 2HA  GLY    2    -2.204 0.281 3.887
ATOM    12  C GLY    2    -1.017 2.039 4.164
ATOM    13  O GLY    2    -1.434 3.101 4.622
ATOM    14  N ALA    3    0.223 1.594 4.378
ATOM    15  H ALA    3    0.505 0.713 3.974
ATOM    16  CA  ALA    3    1.177 2.339 5.175
ATOM    17  HA  ALA    3    0.759 2.410 6.179
ATOM    18  C ALA    3    1.399 3.732 4.602
ATOM    19  O ALA    3    1.381 4.718 5.335
ATOM    20  CB  ALA    3    2.527 1.632 5.218
ATOM    21 1HB  ALA    3    3.223 2.214 5.823
ATOM    22 2HB  ALA    3    2.405 0.642 5.657
ATOM    23 3HB  ALA    3    2.919 1.535 4.206
ATOM    24  N GLY    4    1.610 3.810 3.286
ATOM    25  H GLY    4    1.613 2.962 2.738
ATOM    26  CA  GLY    4    1.835 5.078 2.621
ATOM    27 1HA  GLY    4    2.746 5.534 3.007
ATOM    28 2HA  GLY    4    1.936 4.901 1.550
ATOM    29  C GLY    4    0.659 6.016 2.855
ATOM    30  O GLY    4    0.850 7.182 3.194
ATOM    31  N NME    5    -0.560 5.503 2.675
ATOM    32  H NME    5    -0.649 4.537 2.396
ATOM    33  CA  NME    5    -1.759 6.294 2.866
ATOM    34 1HA  NME    5    -1.484 7.306 3.163
ATOM    35 2HA  NME    5    -2.324 6.329 1.935
ATOM    36 3HA  NME    5    -2.372 5.841 3.646
CONECT 1 2
CONECT 2 1 3 4 5
CONECT 3 2
CONECT 4 2
CONECT 5 2 6 7
CONECT 6 5
CONECT 7 8 5 9
CONECT 8 7
CONECT 9 7 10 11 12
CONECT 10 9
CONECT 11 9
CONECT 12 9 13 14
CONECT 13 12
CONECT 14 15 12 16
CONECT 15 14
CONECT 16 14 17 18 20
CONECT 17 16
CONECT 18 16 19 24
CONECT 19 18
CONECT 20 16 21 22 23
CONECT 21 20
CONECT 22 20
CONECT 23 20
CONECT 24 25 18 26
CONECT 25 24
CONECT 26 24 27 28 29
CONECT 27 26
CONECT 28 26
CONECT 29 26 30 31
CONECT 30 29
CONECT 31 32 29 33
CONECT 32 31
CONECT 33 31 34 35 36
CONECT 34 33
CONECT 35 33
CONECT 36 33
END

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