计算化学公社
标题:
求助：solvate填充水分子，为什么出现四角填不满的现象？
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作者Author:
黄飞
时间:
2021-8-15 11:14
标题:
求助：solvate填充水分子，为什么出现四角填不满的现象？
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作者Author:
sobereva
时间:
2021-8-15 19:59
把具体的命令贴出来，涉及的文件也上传便于别人重复
作者Author:
黄飞
时间:
2021-8-15 20:57
好的，老师。首先用packmol <cel_solvents.inp构建50*50*50大分子体系，然后通过gmx solvate -cp mix.pdb -o mix.gro向盒子中填充水分子，通过VMD查看就出现这种空缺情况。相关文件如下：
cel_solvents.inp:
tolerance 2.0
filetype pdb
output mix.pdb
add_box_sides
structure cel.pdb
number 4
inside box 0 0 0 50 50 50
end structure
cel.pdb:
CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1
ATOM 1 HO1 ROH 1 13.150 33.572 48.184 0.00 0.00 M30 H
ATOM 2 O1 ROH 1 12.306 33.225 48.379 0.00 0.00 M30 O
ATOM 3 C1 4GB 2 11.707 32.935 47.159 1.00 0.00 M30 C
ATOM 4 H1 4GB 2 10.761 32.746 47.331 1.00 0.00 M30 H
ATOM 5 O5 4GB 2 12.382 31.786 46.655 1.00 0.00 M30 O
ATOM 6 C5 4GB 2 11.800 31.298 45.431 1.00 0.00 M30 C
ATOM 7 H5 4GB 2 10.850 31.109 45.579 1.00 0.00 M30 H
ATOM 8 C6 4GB 2 12.516 29.994 45.122 1.00 0.00 M30 C
ATOM 9 H62 4GB 2 12.531 29.438 45.916 1.00 0.00 M30 H
ATOM 10 H61 4GB 2 13.431 30.182 44.864 1.00 0.00 M30 H
ATOM 11 O6 4GB 2 11.855 29.309 44.073 1.00 0.00 M30 O
ATOM 12 H6O 4GB 2 12.424 28.581 43.752 1.00 0.00 M30 H
ATOM 13 C4 4GB 2 11.937 32.349 44.375 1.00 0.00 M30 C
ATOM 14 H4 4GB 2 12.895 32.450 44.193 1.00 0.00 M30 H
ATOM 15 C3 4GB 2 11.416 33.709 44.792 1.00 0.00 M30 C
ATOM 16 H3 4GB 2 10.434 33.671 44.800 1.00 0.00 M30 H
ATOM 17 O3 4GB 2 11.822 34.720 43.846 1.00 0.00 M30 O
ATOM 18 H3O 4GB 2 11.262 34.549 43.059 1.00 0.00 M30 H
ATOM 19 C2 4GB 2 11.886 34.092 46.174 1.00 0.00 M30 C
ATOM 20 H2 4GB 2 12.826 34.367 46.143 1.00 0.00 M30 H
ATOM 21 O2 4GB 2 11.088 35.152 46.707 1.00 0.00 M30 O
ATOM 22 H2O 4GB 2 11.273 35.196 47.665 1.00 0.00 M30 H
ATOM 23 O4 4GB 2 11.319 31.892 43.156 1.00 0.00 M30 O
ATOM 24 C1 4GB 3 12.002 32.251 41.969 1.00 0.00 M30 C
ATOM 25 H1 4GB 3 12.948 32.440 42.141 1.00 0.00 M30 H
ATOM 26 O5 4GB 3 11.327 33.400 41.465 1.00 0.00 M30 O
ATOM 27 C5 4GB 3 11.909 33.889 40.241 1.00 0.00 M30 C
ATOM 28 H5 4GB 3 12.858 34.077 40.389 1.00 0.00 M30 H
ATOM 29 C6 4GB 3 11.192 35.192 39.932 1.00 0.00 M30 C
ATOM 30 H62 4GB 3 11.178 35.748 40.726 1.00 0.00 M30 H
ATOM 31 H61 4GB 3 10.278 35.004 39.674 1.00 0.00 M30 H
ATOM 32 O6 4GB 3 11.854 35.877 38.883 1.00 0.00 M30 O
ATOM 33 H6O 4GB 3 11.285 36.605 38.562 1.00 0.00 M30 H
ATOM 34 C4 4GB 3 11.772 32.838 39.185 1.00 0.00 M30 C
ATOM 35 H4 4GB 3 10.814 32.737 39.003 1.00 0.00 M30 H
ATOM 36 C3 4GB 3 12.293 31.477 39.602 1.00 0.00 M30 C
ATOM 37 H3 4GB 3 13.275 31.515 39.610 1.00 0.00 M30 H
ATOM 38 O3 4GB 3 11.887 30.466 38.656 1.00 0.00 M30 O
ATOM 39 H3O 4GB 3 12.447 30.638 37.869 1.00 0.00 M30 H
ATOM 40 C2 4GB 3 11.823 31.094 40.984 1.00 0.00 M30 C
ATOM 41 H2 4GB 3 10.883 30.819 40.953 1.00 0.00 M30 H
ATOM 42 O2 4GB 3 12.621 30.035 41.517 1.00 0.00 M30 O
ATOM 43 H2O 4GB 3 12.436 29.991 42.475 1.00 0.00 M30 H
ATOM 44 O4 4GB 3 12.390 33.294 37.966 1.00 0.00 M30 O
ATOM 45 C1 4GB 4 11.707 32.935 36.779 1.00 0.00 M30 C
ATOM 46 H1 4GB 4 10.761 32.746 36.951 1.00 0.00 M30 H
ATOM 47 O5 4GB 4 12.382 31.786 36.275 1.00 0.00 M30 O
ATOM 48 C5 4GB 4 11.800 31.298 35.051 1.00 0.00 M30 C
ATOM 49 H5 4GB 4 10.850 31.109 35.199 1.00 0.00 M30 H
ATOM 50 C6 4GB 4 12.516 29.994 34.742 1.00 0.00 M30 C
ATOM 51 H62 4GB 4 12.531 29.438 35.536 1.00 0.00 M30 H
ATOM 52 H61 4GB 4 13.431 30.182 34.484 1.00 0.00 M30 H
ATOM 53 O6 4GB 4 11.855 29.309 33.693 1.00 0.00 M30 O
ATOM 54 H6O 4GB 4 12.424 28.581 33.372 1.00 0.00 M30 H
ATOM 55 C4 4GB 4 11.937 32.349 33.994 1.00 0.00 M30 C
ATOM 56 H4 4GB 4 12.895 32.450 33.813 1.00 0.00 M30 H
ATOM 57 C3 4GB 4 11.416 33.709 34.412 1.00 0.00 M30 C
ATOM 58 H3 4GB 4 10.434 33.671 34.420 1.00 0.00 M30 H
ATOM 59 O3 4GB 4 11.822 34.720 33.466 1.00 0.00 M30 O
ATOM 60 H3O 4GB 4 11.262 34.549 32.679 1.00 0.00 M30 H
ATOM 61 C2 4GB 4 11.886 34.092 35.794 1.00 0.00 M30 C
ATOM 62 H2 4GB 4 12.826 34.367 35.763 1.00 0.00 M30 H
ATOM 63 O2 4GB 4 11.088 35.152 36.327 1.00 0.00 M30 O
ATOM 64 H2O 4GB 4 11.273 35.196 37.285 1.00 0.00 M30 H
ATOM 65 O4 4GB 4 11.319 31.892 32.776 1.00 0.00 M30 O
ATOM 66 C1 4GB 5 12.002 32.251 31.589 1.00 0.00 M30 C
ATOM 67 H1 4GB 5 12.948 32.440 31.761 1.00 0.00 M30 H
ATOM 68 O5 4GB 5 11.327 33.400 31.085 1.00 0.00 M30 O
ATOM 69 C5 4GB 5 11.909 33.889 29.861 1.00 0.00 M30 C
ATOM 70 H5 4GB 5 12.858 34.077 30.009 1.00 0.00 M30 H
ATOM 71 C6 4GB 5 11.192 35.192 29.552 1.00 0.00 M30 C
ATOM 72 H62 4GB 5 11.178 35.748 30.346 1.00 0.00 M30 H
ATOM 73 H61 4GB 5 10.278 35.004 29.294 1.00 0.00 M30 H
ATOM 74 O6 4GB 5 11.854 35.877 28.503 1.00 0.00 M30 O
ATOM 75 H6O 4GB 5 11.285 36.605 28.182 1.00 0.00 M30 H
ATOM 76 C4 4GB 5 11.772 32.838 28.805 1.00 0.00 M30 C
ATOM 77 H4 4GB 5 10.814 32.737 28.623 1.00 0.00 M30 H
ATOM 78 C3 4GB 5 12.293 31.477 29.222 1.00 0.00 M30 C
ATOM 79 H3 4GB 5 13.275 31.515 29.230 1.00 0.00 M30 H
ATOM 80 O3 4GB 5 11.887 30.466 28.276 1.00 0.00 M30 O
ATOM 81 H3O 4GB 5 12.447 30.638 27.489 1.00 0.00 M30 H
ATOM 82 C2 4GB 5 11.823 31.094 30.604 1.00 0.00 M30 C
ATOM 83 H2 4GB 5 10.883 30.819 30.573 1.00 0.00 M30 H
ATOM 84 O2 4GB 5 12.621 30.035 31.137 1.00 0.00 M30 O
ATOM 85 H2O 4GB 5 12.436 29.991 32.095 1.00 0.00 M30 H
ATOM 86 O4 4GB 5 12.390 33.294 27.586 1.00 0.00 M30 O
ATOM 87 C1 4GB 6 11.707 32.935 26.399 1.00 0.00 M30 C
ATOM 88 H1 4GB 6 10.761 32.746 26.571 1.00 0.00 M30 H
ATOM 89 O5 4GB 6 12.382 31.786 25.895 1.00 0.00 M30 O
ATOM 90 C5 4GB 6 11.800 31.298 24.671 1.00 0.00 M30 C
ATOM 91 H5 4GB 6 10.850 31.109 24.819 1.00 0.00 M30 H
ATOM 92 C6 4GB 6 12.516 29.994 24.362 1.00 0.00 M30 C
ATOM 93 H62 4GB 6 12.531 29.438 25.156 1.00 0.00 M30 H
ATOM 94 H61 4GB 6 13.431 30.182 24.104 1.00 0.00 M30 H
ATOM 95 O6 4GB 6 11.855 29.309 23.313 1.00 0.00 M30 O
ATOM 96 H6O 4GB 6 12.424 28.581 22.992 1.00 0.00 M30 H
ATOM 97 C4 4GB 6 11.937 32.349 23.615 1.00 0.00 M30 C
ATOM 98 H4 4GB 6 12.895 32.450 23.433 1.00 0.00 M30 H
ATOM 99 C3 4GB 6 11.416 33.709 24.032 1.00 0.00 M30 C
ATOM 100 H3 4GB 6 10.434 33.671 24.040 1.00 0.00 M30 H
ATOM 101 O3 4GB 6 11.822 34.720 23.086 1.00 0.00 M30 O
ATOM 102 H3O 4GB 6 11.262 34.549 22.299 1.00 0.00 M30 H
ATOM 103 C2 4GB 6 11.886 34.092 25.414 1.00 0.00 M30 C
ATOM 104 H2 4GB 6 12.826 34.367 25.383 1.00 0.00 M30 H
ATOM 105 O2 4GB 6 11.088 35.152 25.947 1.00 0.00 M30 O
ATOM 106 H2O 4GB 6 11.273 35.196 26.905 1.00 0.00 M30 H
ATOM 107 O4 4GB 6 11.319 31.892 22.396 1.00 0.00 M30 O
ATOM 108 C1 4GB 7 12.002 32.251 21.209 1.00 0.00 M30 C
ATOM 109 H1 4GB 7 12.948 32.440 21.381 1.00 0.00 M30 H
ATOM 110 O5 4GB 7 11.327 33.400 20.705 1.00 0.00 M30 O
ATOM 111 C5 4GB 7 11.909 33.889 19.481 1.00 0.00 M30 C
ATOM 112 H5 4GB 7 12.858 34.077 19.629 1.00 0.00 M30 H
ATOM 113 C6 4GB 7 11.192 35.192 19.172 1.00 0.00 M30 C
ATOM 114 H62 4GB 7 11.178 35.748 19.966 1.00 0.00 M30 H
ATOM 115 H61 4GB 7 10.278 35.004 18.914 1.00 0.00 M30 H
ATOM 116 O6 4GB 7 11.854 35.877 18.123 1.00 0.00 M30 O
ATOM 117 H6O 4GB 7 11.285 36.605 17.802 1.00 0.00 M30 H
ATOM 118 C4 4GB 7 11.772 32.838 18.424 1.00 0.00 M30 C
ATOM 119 H4 4GB 7 10.814 32.737 18.243 1.00 0.00 M30 H
ATOM 120 C3 4GB 7 12.293 31.477 18.842 1.00 0.00 M30 C
ATOM 121 H3 4GB 7 13.275 31.515 18.850 1.00 0.00 M30 H
ATOM 122 O3 4GB 7 11.887 30.466 17.896 1.00 0.00 M30 O
ATOM 123 H3O 4GB 7 12.447 30.638 17.109 1.00 0.00 M30 H
ATOM 124 C2 4GB 7 11.823 31.094 20.224 1.00 0.00 M30 C
ATOM 125 H2 4GB 7 10.883 30.819 20.193 1.00 0.00 M30 H
ATOM 126 O2 4GB 7 12.621 30.035 20.757 1.00 0.00 M30 O
ATOM 127 H2O 4GB 7 12.436 29.991 21.715 1.00 0.00 M30 H
ATOM 128 O4 4GB 7 12.390 33.294 17.206 1.00 0.00 M30 O
ATOM 129 C1 4GB 8 11.707 32.935 16.019 1.00 0.00 M30 C
ATOM 130 H1 4GB 8 10.761 32.746 16.191 1.00 0.00 M30 H
ATOM 131 O5 4GB 8 12.382 31.786 15.515 1.00 0.00 M30 O
ATOM 132 C5 4GB 8 11.800 31.298 14.291 1.00 0.00 M30 C
ATOM 133 H5 4GB 8 10.850 31.109 14.439 1.00 0.00 M30 H
ATOM 134 C6 4GB 8 12.516 29.994 13.982 1.00 0.00 M30 C
ATOM 135 H62 4GB 8 12.531 29.438 14.776 1.00 0.00 M30 H
ATOM 136 H61 4GB 8 13.431 30.182 13.724 1.00 0.00 M30 H
ATOM 137 O6 4GB 8 11.855 29.309 12.933 1.00 0.00 M30 O
ATOM 138 H6O 4GB 8 12.424 28.581 12.612 1.00 0.00 M30 H
ATOM 139 C4 4GB 8 11.937 32.349 13.234 1.00 0.00 M30 C
ATOM 140 H4 4GB 8 12.895 32.450 13.053 1.00 0.00 M30 H
ATOM 141 C3 4GB 8 11.416 33.709 13.652 1.00 0.00 M30 C
ATOM 142 H3 4GB 8 10.434 33.671 13.660 1.00 0.00 M30 H
ATOM 143 O3 4GB 8 11.822 34.720 12.706 1.00 0.00 M30 O
ATOM 144 H3O 4GB 8 11.262 34.549 11.919 1.00 0.00 M30 H
ATOM 145 C2 4GB 8 11.886 34.092 15.034 1.00 0.00 M30 C
ATOM 146 H2 4GB 8 12.826 34.367 15.003 1.00 0.00 M30 H
ATOM 147 O2 4GB 8 11.088 35.152 15.567 1.00 0.00 M30 O
ATOM 148 H2O 4GB 8 11.273 35.196 16.525 1.00 0.00 M30 H
ATOM 149 O4 4GB 8 11.319 31.892 12.016 1.00 0.00 M30 O
ATOM 150 C1 4GB 9 12.002 32.251 10.829 1.00 0.00 M30 C
ATOM 151 H1 4GB 9 12.948 32.440 11.001 1.00 0.00 M30 H
ATOM 152 O5 4GB 9 11.327 33.400 10.325 1.00 0.00 M30 O
ATOM 153 C5 4GB 9 11.909 33.889 9.101 1.00 0.00 M30 C
ATOM 154 H5 4GB 9 12.858 34.077 9.249 1.00 0.00 M30 H
ATOM 155 C6 4GB 9 11.192 35.192 8.792 1.00 0.00 M30 C
ATOM 156 H62 4GB 9 11.178 35.748 9.586 1.00 0.00 M30 H
ATOM 157 H61 4GB 9 10.278 35.004 8.534 1.00 0.00 M30 H
ATOM 158 O6 4GB 9 11.854 35.877 7.743 1.00 0.00 M30 O
ATOM 159 H6O 4GB 9 11.285 36.605 7.422 1.00 0.00 M30 H
ATOM 160 C4 4GB 9 11.772 32.838 8.045 1.00 0.00 M30 C
ATOM 161 H4 4GB 9 10.814 32.737 7.863 1.00 0.00 M30 H
ATOM 162 C3 4GB 9 12.293 31.477 8.462 1.00 0.00 M30 C
ATOM 163 H3 4GB 9 13.275 31.515 8.470 1.00 0.00 M30 H
ATOM 164 O3 4GB 9 11.887 30.466 7.516 1.00 0.00 M30 O
ATOM 165 H3O 4GB 9 12.447 30.638 6.729 1.00 0.00 M30 H
ATOM 166 C2 4GB 9 11.823 31.094 9.844 1.00 0.00 M30 C
ATOM 167 H2 4GB 9 10.883 30.819 9.813 1.00 0.00 M30 H
ATOM 168 O2 4GB 9 12.621 30.035 10.377 1.00 0.00 M30 O
ATOM 169 H2O 4GB 9 12.436 29.991 11.335 1.00 0.00 M30 H
ATOM 170 O4 4GB 9 12.390 33.294 6.826 1.00 0.00 M30 O
ATOM 171 C1 4GB 10 11.707 32.935 5.639 1.00 0.00 M30 C
ATOM 172 H1 4GB 10 10.761 32.746 5.811 1.00 0.00 M30 H
ATOM 173 O5 4GB 10 12.382 31.786 5.135 1.00 0.00 M30 O
ATOM 174 C5 4GB 10 11.800 31.298 3.911 1.00 0.00 M30 C
ATOM 175 H5 4GB 10 10.850 31.109 4.059 1.00 0.00 M30 H
ATOM 176 C6 4GB 10 12.516 29.994 3.602 1.00 0.00 M30 C
ATOM 177 H62 4GB 10 12.531 29.438 4.396 1.00 0.00 M30 H
ATOM 178 H61 4GB 10 13.431 30.182 3.344 1.00 0.00 M30 H
ATOM 179 O6 4GB 10 11.855 29.309 2.553 1.00 0.00 M30 O
ATOM 180 H6O 4GB 10 12.424 28.581 2.232 1.00 0.00 M30 H
ATOM 181 C4 4GB 10 11.937 32.349 2.855 1.00 0.00 M30 C
ATOM 182 H4 4GB 10 12.895 32.450 2.673 1.00 0.00 M30 H
ATOM 183 C3 4GB 10 11.416 33.709 3.272 1.00 0.00 M30 C
ATOM 184 H3 4GB 10 10.434 33.671 3.280 1.00 0.00 M30 H
ATOM 185 O3 4GB 10 11.822 34.720 2.326 1.00 0.00 M30 O
ATOM 186 H3O 4GB 10 11.262 34.549 1.539 1.00 0.00 M30 H
ATOM 187 C2 4GB 10 11.886 34.092 4.654 1.00 0.00 M30 C
ATOM 188 H2 4GB 10 12.826 34.367 4.623 1.00 0.00 M30 H
ATOM 189 O2 4GB 10 11.088 35.152 5.187 1.00 0.00 M30 O
ATOM 190 H2O 4GB 10 11.273 35.196 6.145 1.00 0.00 M30 H
ATOM 191 O4 4GB 10 11.319 31.892 1.636 1.00 0.00 M30 O
ATOM 192 C1 0GB 11 12.002 32.251 0.449 1.00 0.00 M30 C
ATOM 193 H1 0GB 11 12.948 32.440 0.621 1.00 0.00 M30 H
ATOM 194 O5 0GB 11 11.327 33.400 -0.055 1.00 0.00 M30 O
ATOM 195 C5 0GB 11 11.909 33.889 -1.279 1.00 0.00 M30 C
ATOM 196 H5 0GB 11 12.858 34.077 -1.131 1.00 0.00 M30 H
ATOM 197 C6 0GB 11 11.192 35.192 -1.588 1.00 0.00 M30 C
ATOM 198 H62 0GB 11 11.178 35.748 -0.794 1.00 0.00 M30 H
ATOM 199 H61 0GB 11 10.278 35.004 -1.846 1.00 0.00 M30 H
ATOM 200 O6 0GB 11 11.854 35.877 -2.637 1.00 0.00 M30 O
ATOM 201 H6O 0GB 11 11.285 36.605 -2.958 1.00 0.00 M30 H
ATOM 202 C4 0GB 11 11.772 32.838 -2.336 1.00 0.00 M30 C
ATOM 203 H4 0GB 11 10.814 32.737 -2.517 1.00 0.00 M30 H
ATOM 204 O4 0GB 11 12.390 33.294 -3.554 1.00 0.00 M30 O
ATOM 205 H4O 0GB 11 12.374 32.563 -4.223 0.00 0.00 M30 H
ATOM 206 C3 0GB 11 12.293 31.477 -1.918 1.00 0.00 M30 C
ATOM 207 H3 0GB 11 13.275 31.515 -1.910 1.00 0.00 M30 H
ATOM 208 O3 0GB 11 11.887 30.466 -2.864 1.00 0.00 M30 O
ATOM 209 H3O 0GB 11 12.447 30.638 -3.651 1.00 0.00 M30 H
ATOM 210 C2 0GB 11 11.823 31.094 -0.536 1.00 0.00 M30 C
ATOM 211 H2 0GB 11 10.883 30.819 -0.567 1.00 0.00 M30 H
ATOM 212 O2 0GB 11 12.621 30.035 -0.003 1.00 0.00 M30 O
ATOM 213 H2O 0GB 11 12.436 29.991 0.955 1.00 0.00 M30 H
END
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