pdb文件到gro不正常，小分子配体散架

CLS1993 · 发表于 Post on 2024-2-8 16:39:40

我按照教程做，出来的gro很正常，我用我自己的，我的小分子配体就散架了，不知道为什么
以下是我的文件pdb
ATOM    1 C1 isoborn 1    6.204  32.278 -48.884  1.00  0.00
ATOM    2 C2 isoborn 1    7.061  32.868 -47.754  1.00  0.00
ATOM    3 C3 isoborn 1    7.914  31.669 -47.306  1.00  0.00
ATOM    4 C4 isoborn 1    8.951  31.363 -48.400  1.00  0.00
ATOM    5 C5 isoborn 1    8.095  30.773 -49.531  1.00  0.00
ATOM    6 C6 isoborn 1    6.674  30.814 -48.945  1.00  0.00
ATOM    7 C7 isoborn 1    6.934  30.508 -47.471  1.00  0.00
ATOM    8 C8 isoborn 1    7.573  29.144 -47.243  1.00  0.00
ATOM    9 C9 isoborn 1    5.744  30.421 -46.525  1.00  0.00
ATOM    10 C10  isoborn 1    5.704  29.924 -49.711  1.00  0.00
ATOM    11 O11  isoborn 1    8.483  29.457 -49.822  1.00  0.00
ATOM    12 H1 isoborn 1    7.758  29.051 -50.266  1.00  0.00
ATOM    13 H2 isoborn 1    6.390  32.781 -49.810  1.00  0.00
ATOM    14 H3 isoborn 1    5.153  32.377 -48.712  1.00  0.00
ATOM    15 H4 isoborn 1    6.448  33.225 -46.953  1.00  0.00
ATOM    16 H5 isoborn 1    7.645  33.710 -48.063  1.00  0.00
ATOM    17 H6 isoborn 1    8.364  31.824 -46.348  1.00  0.00
ATOM    18 H7 isoborn 1    9.675  30.654 -48.056  1.00  0.00
ATOM    19 H8 isoborn 1    9.513  32.222 -48.701  1.00  0.00
ATOM    20 H9 isoborn 1    8.187  31.308 -50.453  1.00  0.00
ATOM    21 H10  isoborn 1    8.446  29.052 -47.855  1.00  0.00
ATOM    22 H11  isoborn 1    6.874  28.375 -47.500  1.00  0.00
ATOM    23 H12  isoborn 1    7.848  29.047 -46.214  1.00  0.00
ATOM    24 H13  isoborn 1    5.182  31.330 -46.574  1.00  0.00
ATOM    25 H14  isoborn 1    6.094  30.271 -45.525  1.00  0.00
ATOM    26 H15  isoborn 1    5.120  29.600 -46.811  1.00  0.00
ATOM    27 H16  isoborn 1    5.630  30.265 -50.722  1.00  0.00
ATOM    28 H17  isoborn 1    4.740  29.966 -49.249  1.00  0.00
ATOM    29 H18  isoborn 1    6.061  28.915 -49.700  1.00  0.00
END
出来的gro
GROningen MAchine for Chemical Simulation
29
0isob C1 1 0.600  20.400  27.800
0isob C2 2 0.700 6.100  86.800
0isob C3 3 0.700  91.400  66.900
0isob C4 4 0.800  95.100  36.300
0isob C5 5 0.800 9.500  77.300
0isob C6 6 0.600  67.400  81.400
0isob C7 7 0.600  93.400  50.800
0isob C8 8 0.700  57.300  14.400
0isob C9 9 0.500  74.400  42.100
0isob C10 10 0.500  70.400  92.400
0isob O11 11 0.800  48.300  45.700
0isob H1 12 0.700  75.800 5.100
0isob H2 13 0.600  39.000  78.100
0isob H3 14 0.500  15.300  37.700
0isob H4 15 0.600  44.800  22.500
0isob H5 16 0.700  64.500  71.000
0isob H6 17 0.800  36.400  82.400
0isob H7 18 0.900  67.500  65.400
0isob H8 19 0.900  51.300  22.200
0isob H9 20 0.800  18.700  30.800
0isob H10 21 0.800  44.600 5.200
0isob H11 22 0.600  87.400  37.500
0isob H12 23 0.700  84.800 4.700
0isob H13 24 0.500  18.200  33.000
0isob H14 25 0.600 9.400  27.100
0isob H15 26 0.500  12.000  60.000
0isob H16 27 0.500  63.000  26.500
0isob H17 28 0.400  74.000  96.600
0isob H18 29 0.600 6.100  91.500
0.00000 0.00000 0.00000

sobereva · 发表于 Post on 2024-2-8 20:33:15

CLS1993 发表于 2024-2-8 16:40
用的命令是这个gmx editconf -f jz4_ini.pdb -o jz4.gro

注意论坛的规矩：

有别人回复之前若需要对帖子进行修改、补充，应直接编辑原帖，绝对不要通过回帖进行补充，这点在置顶的新社员必读贴里明确说了。
认真阅读下文再发帖
在网上求助计算化学问题的时候必须把问题描述得详细、具体、准确、清楚
http://sobereva.com/620（http://bbs.keinsci.com/thread-25787-1-1.html）

恰当命名标题，原标题就一句“pdb文件到gro不正常”谁知道你说的是什么情况，完全没说到内容关键点。这次给你改了，下次发帖前认真看http://bbs.keinsci.com/thread-9348-1-1.html

MD过程中分子散架（键长键角变得离谱）通常是拓扑信息、参数有问题，照着http://sobereva.com/soft/Sobtop#FAQ8仔细检查

CLS1993 · 发表于 Post on 2024-2-8 16:41:19

教程里实际如下，我的结果高了好几个量级
pdb：
ATOM    1 C4 JZ4    1    24.294 -24.124  -0.071  1.00  0.00
ATOM    2 C7 JZ4    1    21.553 -27.214  -4.112  1.00  0.00
ATOM    3 C8 JZ4    1    22.068 -26.747  -5.331  1.00  0.00
ATOM    4 C9 JZ4    1    22.671 -25.512  -5.448  1.00  0.00
ATOM    5 C10  JZ4    1    22.769 -24.730  -4.295  1.00  0.00
ATOM    6 C11  JZ4    1    21.693 -26.459  -2.954  1.00  0.00
ATOM    7 C12  JZ4    1    22.294 -25.187  -3.075  1.00  0.00
ATOM    8 C13  JZ4    1    22.463 -24.414  -1.808  1.00  0.00
ATOM    9 C14  JZ4    1    23.925 -24.704  -1.394  1.00  0.00
ATOM    10 OAB  JZ4    1    23.412 -23.536  -4.342  1.00  0.00
ATOM    11 H7 JZ4    1    21.045 -28.166  -4.074  1.00  0.00
ATOM    12 H8 JZ4    1    21.990 -27.375  -6.206  1.00  0.00
ATOM    13 H9 JZ4    1    23.053 -25.163  -6.396  1.00  0.00
ATOM    14 H11  JZ4    1    21.355 -26.831  -1.998  1.00  0.00
ATOM    15 H132 JZ4    1    22.312 -23.348  -1.980  1.00  0.00
ATOM    16 H133 JZ4    1    21.773 -24.777  -1.046  1.00  0.00
ATOM    17 H142 JZ4    1    24.063 -25.784  -1.348  1.00  0.00
ATOM    18 H143 JZ4    1    24.592 -24.297  -2.154  1.00  0.00
ATOM    19 H41  JZ4    1    25.332 -24.366 0.156  1.00  0.00
ATOM    20 H42  JZ4    1    24.172 -23.041  -0.102  1.00  0.00
ATOM    21 H43  JZ4    1    23.647 -24.540 0.701  1.00  0.00
ATOM    22 HAB  JZ4    1    22.822 -22.843  -4.037  1.00  0.00
END
gro：
Gromacs Runs On Most of All Computer Systems GROningen MAchine for Chemical Simulation
22
1JZ4    C4 1 2.429  -2.412  -0.007
1JZ4    C7 2 2.155  -2.721  -0.411
1JZ4    C8 3 2.207  -2.675  -0.533
1JZ4    C9 4 2.267  -2.551  -0.545
1JZ4 C10 5 2.277  -2.473  -0.430
1JZ4 C11 6 2.169  -2.646  -0.295
1JZ4 C12 7 2.229  -2.519  -0.308
1JZ4 C13 8 2.246  -2.441  -0.181
1JZ4 C14 9 2.392  -2.470  -0.139
1JZ4 OAB 10 2.341  -2.354  -0.434
1JZ4    H7 11 2.105  -2.817  -0.407
1JZ4    H8 12 2.199  -2.737  -0.621
1JZ4    H9 13 2.305  -2.516  -0.640
1JZ4 H11 14 2.135  -2.683  -0.200
1JZ4 H132 15 2.231  -2.335  -0.198
1JZ4 H133 16 2.177  -2.478  -0.105
1JZ4 H142 17 2.406  -2.578  -0.135
1JZ4 H143 18 2.459  -2.430  -0.215
1JZ4 H41 19 2.533  -2.437 0.016
1JZ4 H42 20 2.417  -2.304  -0.010
1JZ4 H43 21 2.365  -2.454 0.070
1JZ4 HAB 22 2.282  -2.284  -0.404
0.00000 0.00000 0.00000

CLS1993 · 发表于 Post on 2024-2-8 16:40:19

用的命令是这个gmx editconf -f jz4_ini.pdb -o jz4.gro

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[GROMACS] pdb文件到gro不正常，小分子配体散架