layout: post
title: 自写脚本创建非标准残基蛋白的GROMACS拓扑
categories:
- 科
tags:
- gmx
- amb
chem: true
- 2022-01-06 16:29:39
- 2022-08-10 21:27:45 感谢 周鼎 测试并提供改进意见
几年前, 我写过几篇GROMACS处理非标准残基的教程, 用的是比较正统的方法, 创建非标准残基的rtp文件, 这样基本上可以一劳永逸, 需要的时候只要pdb2gmx就可以了. 但这种方法还是有点繁琐, 步骤很多, 要注意的地方也很多, 一不留心就可能出错. 其次, 这种方法只适合常规的蛋白修饰, 非标准残基只能与前后两个残基相连, 没法使用这种方法将一个非标准残基的两端连接到任意其他残基上. 再者, 有时候我们只是单纯地有一个非标准残基需要处理, 也没想着还会使用它很多次, 或者将它用到别处, 所做的基本上是个一次性的行为. 在这种情况下, 我们用到非标准残基的时候随手创建一下它的拓扑就好了, 就不劳生成什么rtp了, 那还挺麻烦的. 不借助rtp而直接生成包括非标准残基在内的整个体系的拓扑也是可行的, 虽然步骤可能也还是有些繁琐. 我觉得至少有三种方法可以达到目的: 一种是基于ambertools的建模工具和acpype, 一种是基于片段的方法, 一种是直接修改已有拓扑的方法. 第一种暂且不去说它吧, 第二种比较通用, 可以考虑集成到我的gmxtop工具中, 最后一种稍麻烦点, 需要借助一些脚本来完成, 但比起创建rtp的方法还是简单些, 也可以借以理解拓扑的概念, 熟悉拓扑的修改流程, 所以我就花时间写了几个脚本, 以期能达到目的. 由于时间有限, 并没有将几个脚本综合起来并尽量自动化, 因为那与我期望的目的不合, 脚本也会丧失一些通用性.
基础知识
无论创建拓扑还是修改拓扑, 都要先理解拓扑, 理解非键相互作用, 成键相互作用, 其中重点是成键相互作用, 因为非标准残基麻烦的地方就在于会涉及大量成键项原子编号和参数的处理, 除非是只对标准残基进行非常小的修改, 否则大量成键项的处理必须借助脚本或其他自动工具来减轻工作量, 避免错误.
脚本
这几个脚本暂时只能基于我自己的NotepadX运行. 一共有5个脚本, 其中功能相反的脚本实际上可以合并, 通过选项来指定是删除还是保留, 这里明确分开只是为了简单. 此外, 在这篇教程中我们只会用到其中前3个脚本.
2-1_调整top原子编号.js: 调整拓扑中的原子编号2-2_删除top原子.js: 删除拓扑中某些原子及其涉及的成键项2-3_保留top原子.js: 保留拓扑中某些原子及其涉及的成键项2-4_删除top成键项.js: 删除拓扑中的键及其涉及的键角, 二面角项2-5_添加top成键项.js: 添加键及其涉及的键角, 二面角项
如果删除一个原子, 所有涉及删除原子的成键项也必须删除.
如果删除一条键, 所有涉及此键的键角, 二面角项也需要删除. 所涉及的原子是与两个成键原子二级相邻的所有原子. 添加键的情况类似.
<div class="highlight"><pre style="line-height:125%"><span></span> B11 B12
<span style="color: #666666">|</span> <span style="color: #666666">/</span>
A11 B1<span style="color: #666666">--</span>B13
\ <span style="color: #666666">/</span>
A12<span style="color: #666666">--</span>A1<span style="color: #666666">--</span>A<span style="color: #666666">--</span>B<span style="color: #666666">--</span>B2
<span style="color: #666666">/</span> \
A13 B3</pre></div>示例如上图, 删除或添加A-B键时, 涉及
- 键长:
A-B
- 键角:
A-B-B1, A-B-B2, A-B-B3, B-A-A1
- 二面角:
A11-A1-A-B, A12-A1-A-B, A13-A1-A-B, A1-A-B-B1, A1-A-B-B2, A1-A-B-B3, A-B-B1-B11, A-B-B1-B12, A-B-B1-B13
示例
以我常用的小蛋白1crn做示例吧
<figure><script>var Mol1=new ChemDoodle.TransformCanvas3D('Mol-1',502,376.5);Mol1.specs.shapes_color = '#fff';Mol1.specs.backgroundColor = 'black';Mol1.specs.compass_display = true;Mol1.specs.set3DRepresentation('Ball and Stick');Mol1.specs.projectionPerspective_3D = false;Mol1.specs.proteins_ribbonCartoonize = true;Mol1.handle = null;Mol1.timeout = 15;Mol1.specs.crystals_unitCellLineWidth = 1.5;Mol1.specs.nucleics_residueColor = 'rainbow';Mol1.specs.proteins_residueColor= 'rainbow';Mol1.startAnimation = ChemDoodle._AnimatorCanvas.prototype.startAnimation;Mol1.stopAnimation = ChemDoodle._AnimatorCanvas.prototype.stopAnimation;Mol1.isRunning = ChemDoodle._AnimatorCanvas.prototype.isRunning;Mol1.dblclick = ChemDoodle.RotatorCanvas.prototype.dblclick;Mol1.nextFrame = function(delta){var matrix = [];ChemDoodle.lib.mat4.identity(matrix);var change = delta*Math.PI/15000;ChemDoodle.lib.mat4.rotate(matrix,change,[1,0,0]);ChemDoodle.lib.mat4.rotate(matrix,change,[0,1,0]);ChemDoodle.lib.mat4.rotate(matrix,change,[0,0,1]);ChemDoodle.lib.mat4.multiply(this.rotationMatrix, matrix)};var Fmol='HELIX 1 H1 ILE A 7 PRO A 19 13/10 CONFORMATION RES 17,19 13 \nHELIX 2 H2 GLU A 23 THR A 30 1DISTORTED 3/10 AT RES 30 8 \nSHEET 1 S1 2 THR A 1 CYS A 4 0 \nSHEET 2 S1 2 CYS A 32 ILE A 35 -1 \nATOM 1 N THR A 1 17.047 14.099 3.625 1.00 13.79 N \nATOM 2 CA THR A 1 16.967 12.784 4.338 1.00 10.80 C \nATOM 3 C THR A 1 15.685 12.755 5.133 1.00 9.19 C \nATOM 4 O THR A 1 15.268 13.825 5.594 1.00 9.85 O \nATOM 5 CB THR A 1 18.170 12.703 5.337 1.00 13.02 C \nATOM 6 OG1 THR A 1 19.334 12.829 4.463 1.00 15.06 O \nATOM 7 CG2 THR A 1 18.150 11.546 6.304 1.00 14.23 C \nATOM 8 N THR A 2 15.115 11.555 5.265 1.00 7.81 N \nATOM 9 CA THR A 2 13.856 11.469 6.066 1.00 8.31 C \nATOM 10 C THR A 2 14.164 10.785 7.379 1.00 5.80 C \nATOM 11 O THR A 2 14.993 9.862 7.443 1.00 6.94 O \nATOM 12 CB THR A 2 12.732 10.711 5.261 1.00 10.32 C \nATOM 13 OG1 THR A 2 13.308 9.439 4.926 1.00 12.81 O \nATOM 14 CG2 THR A 2 12.484 11.442 3.895 1.00 11.90 C \nATOM 15 N CYS A 3 13.488 11.241 8.417 1.00 5.24 N \nATOM 16 CA CYS A 3 13.660 10.707 9.787 1.00 5.39 C \nATOM 17 C CYS A 3 12.269 10.431 10.323 1.00 4.45 C \nATOM 18 O CYS A 3 11.393 11.308 10.185 1.00 6.54 O \nATOM 19 CB CYS A 3 14.368 11.748 10.691 1.00 5.99 C \nATOM 20 SG CYS A 3 15.885 12.426 10.016 1.00 7.01 S \nATOM 21 N CYS A 4 12.019 9.272 10.928 1.00 3.90 N \nATOM 22 CA CYS A 4 10.646 8.991 11.408 1.00 4.24 C \nATOM 23 C CYS A 4 10.654 8.793 12.919 1.00 3.72 C \nATOM 24 O CYS A 4 11.659 8.296 13.491 1.00 5.30 O \nATOM 25 CB CYS A 4 10.057 7.752 10.682 1.00 4.41 C \nATOM 26 SG CYS A 4 9.837 8.018 8.904 1.00 4.72 S \nATOM 27 N PRO A 5 9.561 9.108 13.563 1.00 3.96 N \nATOM 28 CA PRO A 5 9.448 9.034 15.012 1.00 4.25 C \nATOM 29 C PRO A 5 9.288 7.670 15.606 1.00 4.96 C \nATOM 30 O PRO A 5 9.490 7.519 16.819 1.00 7.44 O \nATOM 31 CB PRO A 5 8.230 9.957 15.345 1.00 5.11 C \nATOM 32 CG PRO A 5 7.338 9.786 14.114 1.00 5.24 C \nATOM 33 CD PRO A 5 8.366 9.804 12.958 1.00 5.20 C \nATOM 34 N SER A 6 8.875 6.686 14.796 1.00 4.83 N \nATOM 35 CA SER A 6 8.673 5.314 15.279 1.00 4.45 C \nATOM 36 C SER A 6 8.753 4.376 14.083 1.00 4.99 C \nATOM 37 O SER A 6 8.726 4.858 12.923 1.00 4.61 O \nATOM 38 CB SER A 6 7.340 5.121 15.996 1.00 5.05 C \nATOM 39 OG SER A 6 6.274 5.220 15.031 1.00 6.39 O \nATOM 40 N ILE A 7 8.881 3.075 14.358 1.00 4.94 N \nATOM 41 CA ILE A 7 8.912 2.083 13.258 1.00 6.33 C \nATOM 42 C ILE A 7 7.581 2.090 12.506 1.00 5.32 C \nATOM 43 O ILE A 7 7.670 2.031 11.245 1.00 6.85 O \nATOM 44 CB ILE A 7 9.207 0.677 13.924 1.00 8.43 C \nATOM 45 CG1 ILE A 7 10.714 0.702 14.312 1.00 9.78 C \nATOM 46 CG2 ILE A 7 8.811 -0.477 12.969 1.00 11.70 C \nATOM 47 CD1 ILE A 7 11.185 -0.516 15.142 1.00 9.92 C \nATOM 48 N VAL A 8 6.458 2.162 13.159 1.00 5.02 N \nATOM 49 CA VAL A 8 5.145 2.209 12.453 1.00 6.93 C \nATOM 50 C VAL A 8 5.115 3.379 11.461 1.00 5.39 C \nATOM 51 O VAL A 8 4.664 3.268 10.343 1.00 6.30 O \nATOM 52 CB VAL A 8 3.995 2.354 13.478 1.00 9.64 C \nATOM 53 CG1 VAL A 8 2.716 2.891 12.869 1.00 13.85 C \nATOM 54 CG2 VAL A 8 3.758 1.032 14.208 1.00 11.97 C \nATOM 55 N ALA A 9 5.606 4.546 11.941 1.00 3.73 N \nATOM 56 CA ALA A 9 5.598 5.767 11.082 1.00 3.56 C \nATOM 57 C ALA A 9 6.441 5.527 9.850 1.00 4.13 C \nATOM 58 O ALA A 9 6.052 5.933 8.744 1.00 4.36 O \nATOM 59 CB ALA A 9 6.022 6.977 11.891 1.00 4.80 C \nATOM 60 N ARG A 10 7.647 4.909 10.005 1.00 3.73 N \nATOM 61 CA ARG A 10 8.496 4.609 8.837 1.00 3.38 C \nATOM 62 C ARG A 10 7.798 3.609 7.876 1.00 3.47 C \nATOM 63 O ARG A 10 7.878 3.778 6.651 1.00 4.67 O \nATOM 64 CB ARG A 10 9.847 4.020 9.305 1.00 3.95 C \nATOM 65 CG ARG A 10 10.752 3.607 8.149 1.00 4.55 C \nATOM 66 CD ARG A 10 11.226 4.699 7.244 1.00 5.89 C \nATOM 67 NE ARG A 10 12.143 5.571 8.035 1.00 6.20 N \nATOM 68 CZ ARG A 10 12.758 6.609 7.443 1.00 7.52 C \nATOM 69 NH1 ARG A 10 12.539 6.932 6.158 1.00 10.68 N \nATOM 70 NH2 ARG A 10 13.601 7.322 8.202 1.00 9.48 N \nATOM 71 N SER A 11 7.186 2.582 8.445 1.00 5.19 N \nATOM 72 CA SER A 11 6.500 1.584 7.565 1.00 4.60 C \nATOM 73 C SER A 11 5.382 2.313 6.773 1.00 4.84 C \nATOM 74 O SER A 11 5.213 2.016 5.557 1.00 5.84 O \nATOM 75 CB SER A 11 5.908 0.462 8.400 1.00 5.91 C \nATOM 76 OG SER A 11 6.990 -0.272 9.012 1.00 8.38 O \nATOM 77 N ASN A 12 4.648 3.182 7.446 1.00 3.54 N \nATOM 78 CA ASN A 12 3.545 3.935 6.751 1.00 4.57 C \nATOM 79 C ASN A 12 4.107 4.851 5.691 1.00 4.14 C \nATOM 80 O ASN A 12 3.536 5.001 4.617 1.00 5.52 O \nATOM 81 CB ASN A 12 2.663 4.677 7.748 1.00 6.42 C \nATOM 82 CG ASN A 12 1.802 3.735 8.610 1.00 8.25 C \nATOM 83 OD1 ASN A 12 1.567 2.613 8.165 1.00 12.72 O \nATOM 84 ND2 ASN A 12 1.394 4.252 9.767 1.00 9.92 N \nATOM 85 N PHE A 13 5.259 5.498 6.005 1.00 3.43 N \nATOM 86 CA PHE A 13 5.929 6.358 5.055 1.00 3.49 C \nATOM 87 C PHE A 13 6.304 5.578 3.799 1.00 3.40 C \nATOM 88 O PHE A 13 6.136 6.072 2.653 1.00 4.07 O \nATOM 89 CB PHE A 13 7.183 6.994 5.754 1.00 5.48 C \nATOM 90 CG PHE A 13 7.884 8.006 4.883 1.00 5.57 C \nATOM 91 CD1 PHE A 13 8.906 7.586 4.027 1.00 6.99 C \nATOM 92 CD2 PHE A 13 7.532 9.373 4.983 1.00 6.52 C \nATOM 93 CE1 PHE A 13 9.560 8.539 3.194 1.00 8.20 C \nATOM 94 CE2 PHE A 13 8.176 10.281 4.145 1.00 6.34 C \nATOM 95 CZ PHE A 13 9.141 9.845 3.292 1.00 6.84 C \nATOM 96 N ASN A 14 6.900 4.390 3.989 1.00 3.64 N \nATOM 97 CA ASN A 14 7.331 3.607 2.791 1.00 4.31 C \nATOM 98 C ASN A 14 6.116 3.210 1.915 1.00 3.98 C \nATOM 99 O ASN A 14 6.240 3.144 0.684 1.00 6.22 O \nATOM 100 CB ASN A 14 8.145 2.404 3.240 1.00 5.81 C \nATOM 101 CG ASN A 14 9.555 2.856 3.730 1.00 6.82 C \nATOM 102 OD1 ASN A 14 10.013 3.895 3.323 1.00 9.43 O \nATOM 103 ND2 ASN A 14 10.120 1.956 4.539 1.00 8.21 N \nATOM 104 N VAL A 15 4.993 2.927 2.571 1.00 3.76 N \nATOM 105 CA VAL A 15 3.782 2.599 1.742 1.00 3.98 C \nATOM 106 C VAL A 15 3.296 3.871 1.004 1.00 3.80 C \nATOM 107 O VAL A 15 2.947 3.817 -0.189 1.00 4.85 O \nATOM 108 CB VAL A 15 2.698 1.953 2.608 1.00 4.71 C \nATOM 109 CG1 VAL A 15 1.384 1.826 1.806 1.00 6.67 C \nATOM 110 CG2 VAL A 15 3.174 0.533 3.005 1.00 6.26 C \nATOM 111 N CYS A 16 3.321 4.987 1.720 1.00 3.79 N \nATOM 112 CA CYS A 16 2.890 6.285 1.126 1.00 3.54 C \nATOM 113 C CYS A 16 3.687 6.597 -0.111 1.00 3.48 C \nATOM 114 O CYS A 16 3.200 7.147 -1.103 1.00 4.63 O \nATOM 115 CB CYS A 16 3.039 7.369 2.240 1.00 4.58 C \nATOM 116 SG CYS A 16 2.559 9.014 1.649 1.00 5.66 S \nATOM 117 N ARG A 17 4.997 6.227 -0.100 1.00 3.99 N \nATOM 118 CA ARG A 17 5.895 6.489 -1.213 1.00 3.83 C \nATOM 119 C ARG A 17 5.738 5.560 -2.409 1.00 3.79 C \nATOM 120 O ARG A 17 6.228 5.901 -3.507 1.00 5.39 O \nATOM 121 CB ARG A 17 7.370 6.507 -0.731 1.00 4.11 C \nATOM 122 CG ARG A 17 7.717 7.687 0.206 1.00 4.69 C \nATOM 123 CD ARG A 17 7.949 8.947 -0.615 1.00 5.10 C \nATOM 124 NE ARG A 17 9.212 8.856 -1.337 1.00 4.71 N \nATOM 125 CZ ARG A 17 9.537 9.533 -2.431 1.00 5.28 C \nATOM 126 NH1 ARG A 17 8.659 10.350 -3.032 1.00 6.67 N \nATOM 127 NH2 ARG A 17 10.793 9.491 -2.899 1.00 6.41 N \nATOM 128 N LEU A 18 5.051 4.411 -2.204 1.00 4.70 N \nATOM 129 CA LEU A 18 4.933 3.431 -3.326 1.00 5.46 C \nATOM 130 C LEU A 18 4.397 4.014 -4.620 1.00 5.13 C \nATOM 131 O LEU A 18 4.988 3.755 -5.687 1.00 5.55 O \nATOM 132 CB LEU A 18 4.196 2.184 -2.863 1.00 6.47 C \nATOM 133 CG LEU A 18 4.960 1.178 -1.991 1.00 7.43 C \nATOM 134 CD1 LEU A 18 3.907 0.097 -1.634 1.00 8.70 C \nATOM 135 CD2 LEU A 18 6.129 0.606 -2.768 1.00 9.39 C \nATOM 136 N PRO A 19 3.329 4.795 -4.543 1.00 4.28 N \nATOM 137 CA PRO A 19 2.792 5.376 -5.797 1.00 5.38 C \nATOM 138 C PRO A 19 3.573 6.540 -6.322 1.00 6.30 C \nATOM 139 O PRO A 19 3.260 7.045 -7.422 1.00 9.62 O \nATOM 140 CB PRO A 19 1.358 5.766 -5.472 1.00 5.87 C \nATOM 141 CG PRO A 19 1.223 5.694 -3.993 1.00 6.47 C \nATOM 142 CD PRO A 19 2.421 4.941 -3.408 1.00 6.45 C \nATOM 143 N GLY A 20 4.565 7.047 -5.559 1.00 4.94 N \nATOM 144 CA GLY A 20 5.366 8.191 -6.018 1.00 5.39 C \nATOM 145 C GLY A 20 5.007 9.481 -5.280 1.00 5.03 C \nATOM 146 O GLY A 20 5.535 10.510 -5.730 1.00 7.34 O \nATOM 147 N THR A 21 4.181 9.438 -4.262 1.00 4.10 N \nATOM 148 CA THR A 21 3.767 10.609 -3.513 1.00 3.94 C \nATOM 149 C THR A 21 5.017 11.397 -3.042 1.00 3.96 C \nATOM 150 O THR A 21 5.947 10.757 -2.523 1.00 5.82 O \nATOM 151 CB THR A 21 2.992 10.188 -2.225 1.00 4.13 C \nATOM 152 OG1 THR A 21 2.051 9.144 -2.623 1.00 5.45 O \nATOM 153 CG2 THR A 21 2.260 11.349 -1.551 1.00 5.41 C \nATOM 154 N PRO A 22 4.971 12.703 -3.176 1.00 5.04 N \nATOM 155 CA PRO A 22 6.143 13.513 -2.696 1.00 4.69 C \nATOM 156 C PRO A 22 6.400 13.233 -1.225 1.00 4.19 C \nATOM 157 O PRO A 22 5.485 13.061 -0.382 1.00 4.47 O \nATOM 158 CB PRO A 22 5.703 14.969 -2.920 1.00 7.12 C \nATOM 159 CG PRO A 22 4.676 14.893 -3.996 1.00 7.03 C \nATOM 160 CD PRO A 22 3.964 13.567 -3.811 1.00 4.90 C \nATOM 161 N GLU A 23 7.728 13.297 -0.921 1.00 5.16 N \nATOM 162 CA GLU A 23 8.114 13.103 0.500 1.00 5.31 C \nATOM 163 C GLU A 23 7.427 14.073 1.410 1.00 4.11 C \nATOM 164 O GLU A 23 7.036 13.682 2.540 1.00 5.11 O \nATOM 165 CB GLU A 23 9.648 13.285 0.660 1.00 6.16 C \nATOM 166 CG GLU A 23 10.440 12.093 0.063 1.00 7.48 C \nATOM 167 CD GLU A 23 11.941 12.170 0.391 1.00 9.40 C \nATOM 168 OE1 GLU A 23 12.416 13.225 0.681 1.00 10.40 O \nATOM 169 OE2 GLU A 23 12.539 11.070 0.292 1.00 13.32 O \nATOM 170 N ALA A 24 7.212 15.334 0.966 1.00 4.56 N \nATOM 171 CA ALA A 24 6.614 16.317 1.913 1.00 4.49 C \nATOM 172 C ALA A 24 5.212 15.936 2.350 1.00 4.10 C \nATOM 173 O ALA A 24 4.782 16.166 3.495 1.00 5.64 O \nATOM 174 CB ALA A 24 6.605 17.695 1.246 1.00 5.80 C \nATOM 175 N ILE A 25 4.445 15.318 1.405 1.00 4.37 N \nATOM 176 CA ILE A 25 3.074 14.894 1.756 1.00 5.44 C \nATOM 177 C ILE A 25 3.085 13.643 2.645 1.00 4.32 C \nATOM 178 O ILE A 25 2.315 13.523 3.578 1.00 4.72 O \nATOM 179 CB ILE A 25 2.204 14.637 0.462 1.00 6.42 C \nATOM 180 CG1 ILE A 25 1.815 16.048 -0.129 1.00 7.50 C \nATOM 181 CG2 ILE A 25 0.903 13.864 0.811 1.00 7.65 C \nATOM 182 CD1 ILE A 25 0.756 16.761 0.757 1.00 7.80 C \nATOM 183 N CYS A 26 4.032 12.764 2.313 1.00 3.92 N \nATOM 184 CA CYS A 26 4.180 11.549 3.187 1.00 4.37 C \nATOM 185 C CYS A 26 4.632 11.944 4.596 1.00 3.95 C \nATOM 186 O CYS A 26 4.227 11.252 5.547 1.00 4.74 O \nATOM 187 CB CYS A 26 5.038 10.518 2.539 1.00 4.63 C \nATOM 188 SG CYS A 26 4.349 9.794 1.022 1.00 5.61 S \nATOM 189 N ALA A 27 5.408 13.012 4.694 1.00 3.89 N \nATOM 190 CA ALA A 27 5.879 13.502 6.026 1.00 4.43 C \nATOM 191 C ALA A 27 4.696 13.908 6.882 1.00 4.26 C \nATOM 192 O ALA A 27 4.528 13.422 8.025 1.00 5.44 O \nATOM 193 CB ALA A 27 6.880 14.615 5.830 1.00 5.36 C \nATOM 194 N THR A 28 3.827 14.802 6.358 1.00 4.53 N \nATOM 195 CA THR A 28 2.691 15.221 7.194 1.00 5.08 C \nATOM 196 C THR A 28 1.672 14.132 7.434 1.00 4.62 C \nATOM 197 O THR A 28 0.947 14.112 8.468 1.00 7.80 O \nATOM 198 CB THR A 28 1.986 16.520 6.614 1.00 6.03 C \nATOM 199 OG1 THR A 28 1.664 16.221 5.230 1.00 7.19 O \nATOM 200 CG2 THR A 28 2.914 17.739 6.700 1.00 7.34 C \nATOM 201 N TYR A 29 1.621 13.190 6.511 1.00 5.01 N \nATOM 202 CA TYR A 29 0.715 12.045 6.657 1.00 6.60 C \nATOM 203 C TYR A 29 1.125 11.125 7.815 1.00 4.92 C \nATOM 204 O TYR A 29 0.286 10.632 8.545 1.00 7.13 O \nATOM 205 CB TYR A 29 0.755 11.229 5.322 1.00 9.66 C \nATOM 206 CG TYR A 29 -0.203 10.044 5.354 1.00 11.56 C \nATOM 207 CD1 TYR A 29 -1.547 10.337 5.645 1.00 12.85 C \nATOM 208 CD2 TYR A 29 0.193 8.750 5.100 1.00 14.44 C \nATOM 209 CE1 TYR A 29 -2.496 9.329 5.673 1.00 16.61 C \nATOM 210 CE2 TYR A 29 -0.801 7.705 5.156 1.00 17.11 C \nATOM 211 CZ TYR A 29 -2.079 8.031 5.430 1.00 19.99 C \nATOM 212 OH TYR A 29 -3.097 7.057 5.458 1.00 28.98 O \nATOM 213 N THR A 30 2.470 10.984 7.995 1.00 5.31 N \nATOM 214 CA THR A 30 2.986 9.994 8.950 1.00 5.70 C \nATOM 215 C THR A 30 3.609 10.505 10.230 1.00 6.28 C \nATOM 216 O THR A 30 3.766 9.715 11.186 1.00 8.77 O \nATOM 217 CB THR A 30 4.076 9.103 8.225 1.00 6.55 C \nATOM 218 OG1 THR A 30 5.125 10.027 7.824 1.00 6.57 O \nATOM 219 CG2 THR A 30 3.493 8.324 7.035 1.00 7.29 C \nATOM 220 N GLY A 31 3.984 11.764 10.241 1.00 4.99 N \nATOM 221 CA GLY A 31 4.769 12.336 11.360 1.00 5.50 C \nATOM 222 C GLY A 31 6.255 12.243 11.106 1.00 4.19 C \nATOM 223 O GLY A 31 7.037 12.750 11.954 1.00 6.12 O \nATOM 224 N CYS A 32 6.710 11.631 9.992 1.00 4.30 N \nATOM 225 CA CYS A 32 8.140 11.694 9.635 1.00 4.89 C \nATOM 226 C CYS A 32 8.500 13.141 9.206 1.00 5.50 C \nATOM 227 O CYS A 32 7.581 13.949 8.944 1.00 5.82 O \nATOM 228 CB CYS A 32 8.504 10.686 8.530 1.00 4.66 C \nATOM 229 SG CYS A 32 8.048 8.987 8.881 1.00 5.33 S \nATOM 230 N ILE A 33 9.793 13.410 9.173 1.00 6.02 N \nATOM 231 CA ILE A 33 10.280 14.760 8.823 1.00 5.24 C \nATOM 232 C ILE A 33 11.346 14.658 7.743 1.00 5.16 C \nATOM 233 O ILE A 33 11.971 13.583 7.552 1.00 7.19 O \nATOM 234 CB ILE A 33 10.790 15.535 10.085 1.00 5.49 C \nATOM 235 CG1 ILE A 33 12.059 14.803 10.671 1.00 6.85 C \nATOM 236 CG2 ILE A 33 9.684 15.686 11.138 1.00 6.45 C \nATOM 237 CD1 ILE A 33 12.733 15.676 11.781 1.00 8.94 C \nATOM 238 N ILE A 34 11.490 15.773 7.038 1.00 5.52 N \nATOM 239 CA ILE A 34 12.552 15.877 6.036 1.00 6.82 C \nATOM 240 C ILE A 34 13.590 16.917 6.560 1.00 6.92 C \nATOM 241 O ILE A 34 13.168 18.006 6.945 1.00 9.22 O \nATOM 242 CB ILE A 34 11.987 16.360 4.681 1.00 8.11 C \nATOM 243 CG1 ILE A 34 10.914 15.338 4.163 1.00 9.59 C \nATOM 244 CG2 ILE A 34 13.131 16.517 3.629 1.00 9.73 C \nATOM 245 CD1 ILE A 34 10.151 16.024 2.938 1.00 13.41 C \nATOM 246 N ILE A 35 14.856 16.493 6.536 1.00 7.06 N \nATOM 247 CA ILE A 35 15.930 17.454 6.941 1.00 7.52 C \nATOM 248 C ILE A 35 16.913 17.550 5.819 1.00 6.63 C \nATOM 249 O ILE A 35 17.097 16.660 4.970 1.00 7.90 O \nATOM 250 CB ILE A 35 16.622 16.995 8.285 1.00 8.07 C \nATOM 251 CG1 ILE A 35 17.360 15.651 8.067 1.00 9.41 C \nATOM 252 CG2 ILE A 35 15.592 16.974 9.434 1.00 9.46 C \nATOM 253 CD1 ILE A 35 18.298 15.206 9.219 1.00 9.85 C \nATOM 254 N PRO A 36 17.664 18.669 5.806 1.00 8.07 N \nATOM 255 CA PRO A 36 18.635 18.861 4.738 1.00 8.78 C \nATOM 256 C PRO A 36 19.925 18.042 4.949 1.00 8.31 C \nATOM 257 O PRO A 36 20.593 17.742 3.945 1.00 9.09 O \nATOM 258 CB PRO A 36 18.945 20.364 4.783 1.00 9.67 C \nATOM 259 CG PRO A 36 18.238 20.937 5.908 1.00 10.15 C \nATOM 260 CD PRO A 36 17.371 19.900 6.596 1.00 9.53 C \nATOM 261 N GLY A 37 20.172 17.730 6.217 1.00 8.48 N \nATOM 262 CA GLY A 37 21.452 16.969 6.513 1.00 9.20 C \nATOM 263 C GLY A 37 21.143 15.478 6.427 1.00 10.41 C \nATOM 264 O GLY A 37 20.138 15.023 5.878 1.00 12.06 O \nATOM 265 N ALA A 38 22.055 14.701 7.032 1.00 9.24 N \nATOM 266 CA ALA A 38 22.019 13.242 7.020 1.00 9.24 C \nATOM 267 C ALA A 38 21.944 12.628 8.396 1.00 9.60 C \nATOM 268 O ALA A 38 21.869 11.387 8.435 1.00 13.65 O \nATOM 269 CB ALA A 38 23.246 12.697 6.275 1.00 10.43 C \nATOM 270 N THR A 39 21.894 13.435 9.436 1.00 8.70 N \nATOM 271 CA THR A 39 21.936 12.911 10.809 1.00 9.46 C \nATOM 272 C THR A 39 20.615 13.191 11.521 1.00 8.32 C \nATOM 273 O THR A 39 20.357 14.317 11.948 1.00 9.89 O \nATOM 274 CB THR A 39 23.131 13.601 11.593 1.00 10.72 C \nATOM 275 OG1 THR A 39 24.284 13.401 10.709 1.00 11.66 O \nATOM 276 CG2 THR A 39 23.340 12.935 12.962 1.00 11.81 C \nATOM 277 N CYS A 40 19.827 12.110 11.642 1.00 7.64 N \nATOM 278 CA CYS A 40 18.504 12.312 12.298 1.00 8.05 C \nATOM 279 C CYS A 40 18.684 12.451 13.784 1.00 7.63 C \nATOM 280 O CYS A 40 19.533 11.718 14.362 1.00 9.64 O \nATOM 281 CB CYS A 40 17.582 11.117 11.996 1.00 7.80 C \nATOM 282 SG CYS A 40 17.199 10.929 10.237 1.00 7.30 S \nATOM 283 N PRO A 41 17.880 13.266 14.426 1.00 8.00 N \nATOM 284 CA PRO A 41 17.924 13.421 15.877 1.00 8.96 C \nATOM 285 C PRO A 41 17.392 12.206 16.594 1.00 9.06 C \nATOM 286 O PRO A 41 16.652 11.368 16.033 1.00 8.82 O \nATOM 287 CB PRO A 41 17.076 14.658 16.145 1.00 10.39 C \nATOM 288 CG PRO A 41 16.098 14.689 14.997 1.00 10.99 C \nATOM 289 CD PRO A 41 16.859 14.150 13.779 1.00 10.49 C \nATOM 290 N GLY A 42 17.728 12.124 17.884 1.00 7.55 N \nATOM 291 CA GLY A 42 17.334 10.956 18.691 1.00 8.00 C \nATOM 292 C GLY A 42 15.875 10.688 18.871 1.00 7.22 C \nATOM 293 O GLY A 42 15.434 9.550 19.166 1.00 8.41 O \nATOM 294 N ASP A 43 15.036 11.747 18.715 1.00 5.54 N \nATOM 295 CA ASP A 43 13.564 11.573 18.836 1.00 5.85 C \nATOM 296 C ASP A 43 12.936 11.227 17.470 1.00 5.87 C \nATOM 297 O ASP A 43 11.720 11.040 17.428 1.00 7.29 O \nATOM 298 CB ASP A 43 12.933 12.737 19.580 1.00 6.72 C \nATOM 299 CG ASP A 43 13.140 14.094 18.958 1.00 8.59 C \nATOM 300 OD1 ASP A 43 14.109 14.303 18.212 1.00 9.59 O \nATOM 301 OD2 ASP A 43 12.267 14.963 19.265 1.00 11.45 O \nATOM 302 N TYR A 44 13.725 11.174 16.425 1.00 5.22 N \nATOM 303 CA TYR A 44 13.257 10.745 15.081 1.00 5.56 C \nATOM 304 C TYR A 44 14.275 9.687 14.612 1.00 4.61 C \nATOM 305 O TYR A 44 14.930 9.862 13.568 1.00 6.04 O \nATOM 306 CB TYR A 44 13.200 11.914 14.071 1.00 5.41 C \nATOM 307 CG TYR A 44 12.000 12.819 14.399 1.00 5.34 C \nATOM 308 CD1 TYR A 44 12.119 13.853 15.332 1.00 6.59 C \nATOM 309 CD2 TYR A 44 10.775 12.617 13.762 1.00 5.94 C \nATOM 310 CE1 TYR A 44 11.045 14.675 15.610 1.00 5.97 C \nATOM 311 CE2 TYR A 44 9.676 13.433 14.048 1.00 5.17 C \nATOM 312 CZ TYR A 44 9.802 14.456 14.996 1.00 5.96 C \nATOM 313 OH TYR A 44 8.740 15.265 15.269 1.00 8.60 O \nATOM 314 N ALA A 45 14.342 8.640 15.422 1.00 4.76 N \nATOM 315 CA ALA A 45 15.445 7.667 15.246 1.00 5.89 C \nATOM 316 C ALA A 45 15.171 6.533 14.280 1.00 6.67 C \nATOM 317 O ALA A 45 16.093 5.705 14.039 1.00 7.56 O \nATOM 318 CB ALA A 45 15.680 7.099 16.682 1.00 6.82 C \nATOM 319 N ASN A 46 13.966 6.502 13.739 1.00 5.80 N \nATOM 320 CA ASN A 46 13.512 5.395 12.878 1.00 6.15 C \nATOM 321 C ASN A 46 13.311 5.853 11.455 1.00 6.61 C \nATOM 322 O ASN A 46 13.733 6.929 11.026 1.00 7.18 O \nATOM 323 CB ASN A 46 12.266 4.769 13.501 1.00 7.27 C \nATOM 324 CG ASN A 46 12.538 4.304 14.922 1.00 7.98 C \nATOM 325 OD1 ASN A 46 11.982 4.849 15.886 1.00 11.00 O \nATOM 326 ND2 ASN A 46 13.407 3.298 15.015 1.00 10.32 N \nATOM 327 OXT ASN A 46 12.703 4.973 10.746 1.00 7.86 O \nTER 328 ASN A 46 \n';Mol1.loadMolecule(ChemDoodle.readPDB(Fmol, 1));Mol1.startAnimation();Mol1.stopAnimation();var resType = 'amino';function setDisp1(obj){Mol1.specs["proteins_display"+obj.value]=obj.checked;Mol1.repaint()}function setProj1(yesPers){Mol1.specs.projectionPerspective_3D=yesPers;Mol1.setupScene();Mol1.repaint()}function setColor1(obj){Mol1.specs.proteins_residueColor=resType=obj.value;Mol1.repaint()}function resColor1(obj){this.checked ? Mol1.specs.proteins_residueColor=resType : Mol1.specs.proteins_residueColor='none';Mol1.repaint()}</script><br><span class="meta">视图: <input type="radio" name="group2" onclick="setProj1(true)">投影 <input type="radio" name="group2" onclick="setProj1(false)" checked="">正交<br>着色: <input type="checkbox" onclick="Mol1.specs.macro_colorByChain=this.checked;Mol1.repaint()">按链 <input type="checkbox" onclick="resColor1(this)">按残基<br>模式: <input type="checkbox" value="Ribbon" checked="" onclick="setDisp1(this)">飘带 <input type="checkbox" value="Backbone" onclick="setDisp1(this)">骨架 <input type="checkbox" value="PipePlank" onclick="setDisp1(this)">管板 <input type="checkbox" checked="" onclick="Mol1.specs.proteins_ribbonCartoonize=this.checked;Mol1.repaint()">卡通<br>显示: <input type="checkbox" onclick="Mol1.specs.macro_showWater=this.checked;Mol1.repaint()">水分子 <input type="checkbox" onclick="Mol1.specs.atoms_nonBondedAsStars_3D=this.checked;Mol1.repaint()">非键原子 <input type="checkbox" onclick="Mol1.specs.atoms_displayLabels_3D=this.checked;Mol1.repaint()">名称<br>颜色: <input type="radio" value="amino" name="radio2" onclick="setColor1(this)">氨基酸 <input type="radio" value="shapely" name="radio2" onclick="setColor1(this)">形状 <input type="radio" value="polarity" name="radio2" onclick="setColor1(this)">极性 <input type="radio" value="acidity" name="radio2" onclick="setColor1(this)">酸性 <input type="radio" value="rainbow" name="radio2" onclick="setColor1(this)">彩虹<br>左键: 转动 滚轮: 缩放 双击: 自动旋转开关 Alt+左键: 移动</span><br><figurecaption>Fig.1</figurecaption></figure>这个小蛋白的20号残基原本为20GLY, 我将其侧链与一个常见药物分子布洛芬共价相连, 这样就变成了一个非标准残基, 后文就假定其残基名称为20XXX吧.
<figure><script>var Mol2=new ChemDoodle.TransformCanvas3D('Mol-2',502,376.5);Mol2.specs.shapes_color = '#fff';Mol2.specs.backgroundColor = 'black';Mol2.specs.compass_display = true;Mol2.specs.set3DRepresentation('Ball and Stick');Mol2.specs.projectionPerspective_3D = false;Mol2.specs.proteins_ribbonCartoonize = true;Mol2.handle = null;Mol2.timeout = 15;Mol2.specs.crystals_unitCellLineWidth = 1.5;Mol2.specs.nucleics_residueColor = 'rainbow';Mol2.specs.proteins_residueColor= 'rainbow';Mol2.startAnimation = ChemDoodle._AnimatorCanvas.prototype.startAnimation;Mol2.stopAnimation = ChemDoodle._AnimatorCanvas.prototype.stopAnimation;Mol2.isRunning = ChemDoodle._AnimatorCanvas.prototype.isRunning;Mol2.dblclick = ChemDoodle.RotatorCanvas.prototype.dblclick;Mol2.nextFrame = function(delta){var matrix = [];ChemDoodle.lib.mat4.identity(matrix);var change = delta*Math.PI/15000;ChemDoodle.lib.mat4.rotate(matrix,change,[1,0,0]);ChemDoodle.lib.mat4.rotate(matrix,change,[0,1,0]);ChemDoodle.lib.mat4.rotate(matrix,change,[0,0,1]);ChemDoodle.lib.mat4.multiply(this.rotationMatrix, matrix)};var Fmol='HELIX 1 H1 ILE A 7 PRO A 19 13/10 CONFORMATION RES 17,19 13\nHELIX 2 H2 GLU A 23 THR A 30 1DISTORTED 3/10 AT RES 30 8\nSHEET 1 S1 2 THR A 1 CYS A 4 0\nSHEET 2 S1 2 CYS A 32 ILE A 35 -1\nATOM 1 N THR A 1 17.047 14.099 3.625 1.00 13.79 N\nATOM 2 CA THR A 1 16.967 12.784 4.338 1.00 10.80 C\nATOM 3 C THR A 1 15.685 12.755 5.133 1.00 9.19 C\nATOM 4 O THR A 1 15.268 13.825 5.594 1.00 9.85 O\nATOM 5 CB THR A 1 18.170 12.703 5.337 1.00 13.02 C\nATOM 6 OG1 THR A 1 19.334 12.829 4.463 1.00 15.06 O\nATOM 7 CG2 THR A 1 18.150 11.546 6.304 1.00 14.23 C\nATOM 8 N THR A 2 15.115 11.555 5.265 1.00 7.81 N\nATOM 9 CA THR A 2 13.856 11.469 6.066 1.00 8.31 C\nATOM 10 C THR A 2 14.164 10.785 7.379 1.00 5.80 C\nATOM 11 O THR A 2 14.993 9.862 7.443 1.00 6.94 O\nATOM 12 CB THR A 2 12.732 10.711 5.261 1.00 10.32 C\nATOM 13 OG1 THR A 2 13.308 9.439 4.926 1.00 12.81 O\nATOM 14 CG2 THR A 2 12.484 11.442 3.895 1.00 11.90 C\nATOM 15 N CYS A 3 13.488 11.241 8.417 1.00 5.24 N\nATOM 16 CA CYS A 3 13.660 10.707 9.787 1.00 5.39 C\nATOM 17 C CYS A 3 12.269 10.431 10.323 1.00 4.45 C\nATOM 18 O CYS A 3 11.393 11.308 10.185 1.00 6.54 O\nATOM 19 CB CYS A 3 14.368 11.748 10.691 1.00 5.99 C\nATOM 20 SG CYS A 3 15.885 12.426 10.016 1.00 7.01 S\nATOM 21 N CYS A 4 12.019 9.272 10.928 1.00 3.90 N\nATOM 22 CA CYS A 4 10.646 8.991 11.408 1.00 4.24 C\nATOM 23 C CYS A 4 10.654 8.793 12.919 1.00 3.72 C\nATOM 24 O CYS A 4 11.659 8.296 13.491 1.00 5.30 O\nATOM 25 CB CYS A 4 10.057 7.752 10.682 1.00 4.41 C\nATOM 26 SG CYS A 4 9.837 8.018 8.904 1.00 4.72 S\nATOM 27 N PRO A 5 9.561 9.108 13.563 1.00 3.96 N\nATOM 28 CA PRO A 5 9.448 9.034 15.012 1.00 4.25 C\nATOM 29 C PRO A 5 9.288 7.670 15.606 1.00 4.96 C\nATOM 30 O PRO A 5 9.490 7.519 16.819 1.00 7.44 O\nATOM 31 CB PRO A 5 8.230 9.957 15.345 1.00 5.11 C\nATOM 32 CG PRO A 5 7.338 9.786 14.114 1.00 5.24 C\nATOM 33 CD PRO A 5 8.366 9.804 12.958 1.00 5.20 C\nATOM 34 N SER A 6 8.875 6.686 14.796 1.00 4.83 N\nATOM 35 CA SER A 6 8.673 5.314 15.279 1.00 4.45 C\nATOM 36 C SER A 6 8.753 4.376 14.083 1.00 4.99 C\nATOM 37 O SER A 6 8.726 4.858 12.923 1.00 4.61 O\nATOM 38 CB SER A 6 7.340 5.121 15.996 1.00 5.05 C\nATOM 39 OG SER A 6 6.274 5.220 15.031 1.00 6.39 O\nATOM 40 N ILE A 7 8.881 3.075 14.358 1.00 4.94 N\nATOM 41 CA ILE A 7 8.912 2.083 13.258 1.00 6.33 C\nATOM 42 C ILE A 7 7.581 2.090 12.506 1.00 5.32 C\nATOM 43 O ILE A 7 7.670 2.031 11.245 1.00 6.85 O\nATOM 44 CB ILE A 7 9.207 0.677 13.924 1.00 8.43 C\nATOM 45 CG1 ILE A 7 10.714 0.702 14.312 1.00 9.78 C\nATOM 46 CG2 ILE A 7 8.811 -0.477 12.969 1.00 11.70 C\nATOM 47 CD1 ILE A 7 11.185 -0.516 15.142 1.00 9.92 C\nATOM 48 N VAL A 8 6.458 2.162 13.159 1.00 5.02 N\nATOM 49 CA VAL A 8 5.145 2.209 12.453 1.00 6.93 C\nATOM 50 C VAL A 8 5.115 3.379 11.461 1.00 5.39 C\nATOM 51 O VAL A 8 4.664 3.268 10.343 1.00 6.30 O\nATOM 52 CB VAL A 8 3.995 2.354 13.478 1.00 9.64 C\nATOM 53 CG1 VAL A 8 2.716 2.891 12.869 1.00 13.85 C\nATOM 54 CG2 VAL A 8 3.758 1.032 14.208 1.00 11.97 C\nATOM 55 N ALA A 9 5.606 4.546 11.941 1.00 3.73 N\nATOM 56 CA ALA A 9 5.598 5.767 11.082 1.00 3.56 C\nATOM 57 C ALA A 9 6.441 5.527 9.850 1.00 4.13 C\nATOM 58 O ALA A 9 6.052 5.933 8.744 1.00 4.36 O\nATOM 59 CB ALA A 9 6.022 6.977 11.891 1.00 4.80 C\nATOM 60 N ARG A 10 7.647 4.909 10.005 1.00 3.73 N\nATOM 61 CA ARG A 10 8.496 4.609 8.837 1.00 3.38 C\nATOM 62 C ARG A 10 7.798 3.609 7.876 1.00 3.47 C\nATOM 63 O ARG A 10 7.878 3.778 6.651 1.00 4.67 O\nATOM 64 CB ARG A 10 9.847 4.020 9.305 1.00 3.95 C\nATOM 65 CG ARG A 10 10.752 3.607 8.149 1.00 4.55 C\nATOM 66 CD ARG A 10 11.226 4.699 7.244 1.00 5.89 C\nATOM 67 NE ARG A 10 12.143 5.571 8.035 1.00 6.20 N\nATOM 68 CZ ARG A 10 12.758 6.609 7.443 1.00 7.52 C\nATOM 69 NH1 ARG A 10 12.539 6.932 6.158 1.00 10.68 N\nATOM 70 NH2 ARG A 10 13.601 7.322 8.202 1.00 9.48 N\nATOM 71 N SER A 11 7.186 2.582 8.445 1.00 5.19 N\nATOM 72 CA SER A 11 6.500 1.584 7.565 1.00 4.60 C\nATOM 73 C SER A 11 5.382 2.313 6.773 1.00 4.84 C\nATOM 74 O SER A 11 5.213 2.016 5.557 1.00 5.84 O\nATOM 75 CB SER A 11 5.908 0.462 8.400 1.00 5.91 C\nATOM 76 OG SER A 11 6.990 -0.272 9.012 1.00 8.38 O\nATOM 77 N ASN A 12 4.648 3.182 7.446 1.00 3.54 N\nATOM 78 CA ASN A 12 3.545 3.935 6.751 1.00 4.57 C\nATOM 79 C ASN A 12 4.107 4.851 5.691 1.00 4.14 C\nATOM 80 O ASN A 12 3.536 5.001 4.617 1.00 5.52 O\nATOM 81 CB ASN A 12 2.663 4.677 7.748 1.00 6.42 C\nATOM 82 CG ASN A 12 1.802 3.735 8.610 1.00 8.25 C\nATOM 83 OD1 ASN A 12 1.567 2.613 8.165 1.00 12.72 O\nATOM 84 ND2 ASN A 12 1.394 4.252 9.767 1.00 9.92 N\nATOM 85 N PHE A 13 5.259 5.498 6.005 1.00 3.43 N\nATOM 86 CA PHE A 13 5.929 6.358 5.055 1.00 3.49 C\nATOM 87 C PHE A 13 6.304 5.578 3.799 1.00 3.40 C\nATOM 88 O PHE A 13 6.136 6.072 2.653 1.00 4.07 O\nATOM 89 CB PHE A 13 7.183 6.994 5.754 1.00 5.48 C\nATOM 90 CG PHE A 13 7.884 8.006 4.883 1.00 5.57 C\nATOM 91 CD1 PHE A 13 8.906 7.586 4.027 1.00 6.99 C\nATOM 92 CD2 PHE A 13 7.532 9.373 4.983 1.00 6.52 C\nATOM 93 CE1 PHE A 13 9.560 8.539 3.194 1.00 8.20 C\nATOM 94 CE2 PHE A 13 8.176 10.281 4.145 1.00 6.34 C\nATOM 95 CZ PHE A 13 9.141 9.845 3.292 1.00 6.84 C\nATOM 96 N ASN A 14 6.900 4.390 3.989 1.00 3.64 N\nATOM 97 CA ASN A 14 7.331 3.607 2.791 1.00 4.31 C\nATOM 98 C ASN A 14 6.116 3.210 1.915 1.00 3.98 C\nATOM 99 O ASN A 14 6.240 3.144 0.684 1.00 6.22 O\nATOM 100 CB ASN A 14 8.145 2.404 3.240 1.00 5.81 C\nATOM 101 CG ASN A 14 9.555 2.856 3.730 1.00 6.82 C\nATOM 102 OD1 ASN A 14 10.013 3.895 3.323 1.00 9.43 O\nATOM 103 ND2 ASN A 14 10.120 1.956 4.539 1.00 8.21 N\nATOM 104 N VAL A 15 4.993 2.927 2.571 1.00 3.76 N\nATOM 105 CA VAL A 15 3.782 2.599 1.742 1.00 3.98 C\nATOM 106 C VAL A 15 3.296 3.871 1.004 1.00 3.80 C\nATOM 107 O VAL A 15 2.947 3.817 -0.189 1.00 4.85 O\nATOM 108 CB VAL A 15 2.698 1.953 2.608 1.00 4.71 C\nATOM 109 CG1 VAL A 15 1.384 1.826 1.806 1.00 6.67 C\nATOM 110 CG2 VAL A 15 3.174 0.533 3.005 1.00 6.26 C\nATOM 111 N CYS A 16 3.321 4.987 1.720 1.00 3.79 N\nATOM 112 CA CYS A 16 2.890 6.285 1.126 1.00 3.54 C\nATOM 113 C CYS A 16 3.687 6.597 -0.111 1.00 3.48 C\nATOM 114 O CYS A 16 3.200 7.147 -1.103 1.00 4.63 O\nATOM 115 CB CYS A 16 3.039 7.369 2.240 1.00 4.58 C\nATOM 116 SG CYS A 16 2.559 9.014 1.649 1.00 5.66 S\nATOM 117 N ARG A 17 4.997 6.227 -0.100 1.00 3.99 N\nATOM 118 CA ARG A 17 5.895 6.489 -1.213 1.00 3.83 C\nATOM 119 C ARG A 17 5.738 5.560 -2.409 1.00 3.79 C\nATOM 120 O ARG A 17 6.228 5.901 -3.507 1.00 5.39 O\nATOM 121 CB ARG A 17 7.370 6.507 -0.731 1.00 4.11 C\nATOM 122 CG ARG A 17 7.717 7.687 0.206 1.00 4.69 C\nATOM 123 CD ARG A 17 7.949 8.947 -0.615 1.00 5.10 C\nATOM 124 NE ARG A 17 9.212 8.856 -1.337 1.00 4.71 N\nATOM 125 CZ ARG A 17 9.537 9.533 -2.431 1.00 5.28 C\nATOM 126 NH1 ARG A 17 8.659 10.350 -3.032 1.00 6.67 N\nATOM 127 NH2 ARG A 17 10.793 9.491 -2.899 1.00 6.41 N\nATOM 128 N LEU A 18 5.051 4.411 -2.204 1.00 4.70 N\nATOM 129 CA LEU A 18 4.933 3.431 -3.326 1.00 5.46 C\nATOM 130 C LEU A 18 4.397 4.014 -4.620 1.00 5.13 C\nATOM 131 O LEU A 18 4.988 3.755 -5.687 1.00 5.55 O\nATOM 132 CB LEU A 18 4.196 2.184 -2.863 1.00 6.47 C\nATOM 133 CG LEU A 18 4.960 1.178 -1.991 1.00 7.43 C\nATOM 134 CD1 LEU A 18 3.907 0.097 -1.634 1.00 8.70 C\nATOM 135 CD2 LEU A 18 6.129 0.606 -2.768 1.00 9.39 C\nATOM 136 N PRO A 19 3.329 4.795 -4.543 1.00 4.28 N\nATOM 137 CA PRO A 19 2.792 5.376 -5.797 1.00 5.38 C\nATOM 138 C PRO A 19 3.573 6.540 -6.322 1.00 6.30 C\nATOM 139 O PRO A 19 3.260 7.045 -7.422 1.00 9.62 O\nATOM 140 CB PRO A 19 1.358 5.766 -5.472 1.00 5.87 C\nATOM 141 CG PRO A 19 1.223 5.694 -3.993 1.00 6.47 C\nATOM 142 CD PRO A 19 2.421 4.941 -3.408 1.00 6.45 C\nATOM 143 N GLY A 20 4.565 7.047 -5.559 1.00 4.94 N\nATOM 144 CA GLY A 20 5.366 8.191 -6.018 1.00 5.39 C\nATOM 145 C GLY A 20 5.007 9.481 -5.280 1.00 5.03 C\nATOM 146 O GLY A 20 5.535 10.510 -5.730 1.00 7.34 O\nHETATM 20 C 1 4.803 9.870 -11.977 C\nHETATM 21 C 1 5.547 9.942 -13.162 C\nHETATM 22 C 1 6.945 10.028 -13.109 C\nHETATM 23 C 1 7.599 10.043 -11.869 C\nHETATM 24 C 1 6.855 9.971 -10.684 C\nHETATM 25 C 1 5.457 9.884 -10.737 C\nHETATM 26 H 1 3.736 9.804 -12.018 H\nHETATM 27 H 1 5.048 9.931 -14.109 H\nHETATM 28 H 1 8.666 10.108 -11.828 H\nHETATM 29 H 1 7.355 9.983 -9.738 H\nHETATM 30 C 1 7.762 10.107 -14.412 C\nHETATM 31 H 1 7.181 10.592 -15.168 H\nHETATM 32 C 1 9.052 10.911 -14.161 C\nHETATM 33 H 1 9.620 10.965 -15.066 H\nHETATM 34 H 1 8.799 11.899 -13.838 H\nHETATM 35 H 1 9.633 10.425 -13.405 H\nHETATM 36 C 1 8.125 8.685 -14.877 C\nHETATM 37 O 1 9.186 8.486 -15.523 O\nHETATM 38 O 1 7.257 7.590 -14.574 O\nHETATM 39 H 1 7.773 6.785 -14.489 H\nHETATM 40 C 1 4.640 9.805 -9.435 C\nHETATM 41 C 1 5.476 9.108 -8.346 C\nHETATM 42 C 1 5.840 7.685 -8.811 C\nHETATM 43 H 1 6.372 9.666 -8.171 H\nHETATM 44 H 1 4.944 7.127 -8.985 H\nHETATM 45 H 1 6.407 7.740 -9.716 H\nHETATM 46 H 0 6.420 7.199 -8.055 H\nHETATM 47 C 0 4.660 9.028 -7.043 C\nHETATM 48 H 0 4.406 10.017 -6.720 H\nHETATM 49 H 0 3.763 8.470 -7.218 H\nHETATM 50 H 0 3.744 9.247 -9.609 H\nHETATM 51 H 0 4.388 10.793 -9.112 H\nATOM 147 N THR A 21 4.181 9.438 -4.262 1.00 4.10 N\nATOM 148 CA THR A 21 3.767 10.609 -3.513 1.00 3.94 C\nATOM 149 C THR A 21 5.017 11.397 -3.042 1.00 3.96 C\nATOM 150 O THR A 21 5.947 10.757 -2.523 1.00 5.82 O\nATOM 151 CB THR A 21 2.992 10.188 -2.225 1.00 4.13 C\nATOM 152 OG1 THR A 21 2.051 9.144 -2.623 1.00 5.45 O\nATOM 153 CG2 THR A 21 2.260 11.349 -1.551 1.00 5.41 C\nATOM 154 N PRO A 22 4.971 12.703 -3.176 1.00 5.04 N\nATOM 155 CA PRO A 22 6.143 13.513 -2.696 1.00 4.69 C\nATOM 156 C PRO A 22 6.400 13.233 -1.225 1.00 4.19 C\nATOM 157 O PRO A 22 5.485 13.061 -0.382 1.00 4.47 O\nATOM 158 CB PRO A 22 5.703 14.969 -2.920 1.00 7.12 C\nATOM 159 CG PRO A 22 4.676 14.893 -3.996 1.00 7.03 C\nATOM 160 CD PRO A 22 3.964 13.567 -3.811 1.00 4.90 C\nATOM 161 N GLU A 23 7.728 13.297 -0.921 1.00 5.16 N\nATOM 162 CA GLU A 23 8.114 13.103 0.500 1.00 5.31 C\nATOM 163 C GLU A 23 7.427 14.073 1.410 1.00 4.11 C\nATOM 164 O GLU A 23 7.036 13.682 2.540 1.00 5.11 O\nATOM 165 CB GLU A 23 9.648 13.285 0.660 1.00 6.16 C\nATOM 166 CG GLU A 23 10.440 12.093 0.063 1.00 7.48 C\nATOM 167 CD GLU A 23 11.941 12.170 0.391 1.00 9.40 C\nATOM 168 OE1 GLU A 23 12.416 13.225 0.681 1.00 10.40 O\nATOM 169 OE2 GLU A 23 12.539 11.070 0.292 1.00 13.32 O\nATOM 170 N ALA A 24 7.212 15.334 0.966 1.00 4.56 N\nATOM 171 CA ALA A 24 6.614 16.317 1.913 1.00 4.49 C\nATOM 172 C ALA A 24 5.212 15.936 2.350 1.00 4.10 C\nATOM 173 O ALA A 24 4.782 16.166 3.495 1.00 5.64 O\nATOM 174 CB ALA A 24 6.605 17.695 1.246 1.00 5.80 C\nATOM 175 N ILE A 25 4.445 15.318 1.405 1.00 4.37 N\nATOM 176 CA ILE A 25 3.074 14.894 1.756 1.00 5.44 C\nATOM 177 C ILE A 25 3.085 13.643 2.645 1.00 4.32 C\nATOM 178 O ILE A 25 2.315 13.523 3.578 1.00 4.72 O\nATOM 179 CB ILE A 25 2.204 14.637 0.462 1.00 6.42 C\nATOM 180 CG1 ILE A 25 1.815 16.048 -0.129 1.00 7.50 C\nATOM 181 CG2 ILE A 25 0.903 13.864 0.811 1.00 7.65 C\nATOM 182 CD1 ILE A 25 0.756 16.761 0.757 1.00 7.80 C\nATOM 183 N CYS A 26 4.032 12.764 2.313 1.00 3.92 N\nATOM 184 CA CYS A 26 4.180 11.549 3.187 1.00 4.37 C\nATOM 185 C CYS A 26 4.632 11.944 4.596 1.00 3.95 C\nATOM 186 O CYS A 26 4.227 11.252 5.547 1.00 4.74 O\nATOM 187 CB CYS A 26 5.038 10.518 2.539 1.00 4.63 C\nATOM 188 SG CYS A 26 4.349 9.794 1.022 1.00 5.61 S\nATOM 189 N ALA A 27 5.408 13.012 4.694 1.00 3.89 N\nATOM 190 CA ALA A 27 5.879 13.502 6.026 1.00 4.43 C\nATOM 191 C ALA A 27 4.696 13.908 6.882 1.00 4.26 C\nATOM 192 O ALA A 27 4.528 13.422 8.025 1.00 5.44 O\nATOM 193 CB ALA A 27 6.880 14.615 5.830 1.00 5.36 C\nATOM 194 N THR A 28 3.827 14.802 6.358 1.00 4.53 N\nATOM 195 CA THR A 28 2.691 15.221 7.194 1.00 5.08 C\nATOM 196 C THR A 28 1.672 14.132 7.434 1.00 4.62 C\nATOM 197 O THR A 28 0.947 14.112 8.468 1.00 7.80 O\nATOM 198 CB THR A 28 1.986 16.520 6.614 1.00 6.03 C\nATOM 199 OG1 THR A 28 1.664 16.221 5.230 1.00 7.19 O\nATOM 200 CG2 THR A 28 2.914 17.739 6.700 1.00 7.34 C\nATOM 201 N TYR A 29 1.621 13.190 6.511 1.00 5.01 N\nATOM 202 CA TYR A 29 0.715 12.045 6.657 1.00 6.60 C\nATOM 203 C TYR A 29 1.125 11.125 7.815 1.00 4.92 C\nATOM 204 O TYR A 29 0.286 10.632 8.545 1.00 7.13 O\nATOM 205 CB TYR A 29 0.755 11.229 5.322 1.00 9.66 C\nATOM 206 CG TYR A 29 -0.203 10.044 5.354 1.00 11.56 C\nATOM 207 CD1 TYR A 29 -1.547 10.337 5.645 1.00 12.85 C\nATOM 208 CD2 TYR A 29 0.193 8.750 5.100 1.00 14.44 C\nATOM 209 CE1 TYR A 29 -2.496 9.329 5.673 1.00 16.61 C\nATOM 210 CE2 TYR A 29 -0.801 7.705 5.156 1.00 17.11 C\nATOM 211 CZ TYR A 29 -2.079 8.031 5.430 1.00 19.99 C\nATOM 212 OH TYR A 29 -3.097 7.057 5.458 1.00 28.98 O\nATOM 213 N THR A 30 2.470 10.984 7.995 1.00 5.31 N\nATOM 214 CA THR A 30 2.986 9.994 8.950 1.00 5.70 C\nATOM 215 C THR A 30 3.609 10.505 10.230 1.00 6.28 C\nATOM 216 O THR A 30 3.766 9.715 11.186 1.00 8.77 O\nATOM 217 CB THR A 30 4.076 9.103 8.225 1.00 6.55 C\nATOM 218 OG1 THR A 30 5.125 10.027 7.824 1.00 6.57 O\nATOM 219 CG2 THR A 30 3.493 8.324 7.035 1.00 7.29 C\nATOM 220 N GLY A 31 3.984 11.764 10.241 1.00 4.99 N\nATOM 221 CA GLY A 31 4.769 12.336 11.360 1.00 5.50 C\nATOM 222 C GLY A 31 6.255 12.243 11.106 1.00 4.19 C\nATOM 223 O GLY A 31 7.037 12.750 11.954 1.00 6.12 O\nATOM 224 N CYS A 32 6.710 11.631 9.992 1.00 4.30 N\nATOM 225 CA CYS A 32 8.140 11.694 9.635 1.00 4.89 C\nATOM 226 C CYS A 32 8.500 13.141 9.206 1.00 5.50 C\nATOM 227 O CYS A 32 7.581 13.949 8.944 1.00 5.82 O\nATOM 228 CB CYS A 32 8.504 10.686 8.530 1.00 4.66 C\nATOM 229 SG CYS A 32 8.048 8.987 8.881 1.00 5.33 S\nATOM 230 N ILE A 33 9.793 13.410 9.173 1.00 6.02 N\nATOM 231 CA ILE A 33 10.280 14.760 8.823 1.00 5.24 C\nATOM 232 C ILE A 33 11.346 14.658 7.743 1.00 5.16 C\nATOM 233 O ILE A 33 11.971 13.583 7.552 1.00 7.19 O\nATOM 234 CB ILE A 33 10.790 15.535 10.085 1.00 5.49 C\nATOM 235 CG1 ILE A 33 12.059 14.803 10.671 1.00 6.85 C\nATOM 236 CG2 ILE A 33 9.684 15.686 11.138 1.00 6.45 C\nATOM 237 CD1 ILE A 33 12.733 15.676 11.781 1.00 8.94 C\nATOM 238 N ILE A 34 11.490 15.773 7.038 1.00 5.52 N\nATOM 239 CA ILE A 34 12.552 15.877 6.036 1.00 6.82 C\nATOM 240 C ILE A 34 13.590 16.917 6.560 1.00 6.92 C\nATOM 241 O ILE A 34 13.168 18.006 6.945 1.00 9.22 O\nATOM 242 CB ILE A 34 11.987 16.360 4.681 1.00 8.11 C\nATOM 243 CG1 ILE A 34 10.914 15.338 4.163 1.00 9.59 C\nATOM 244 CG2 ILE A 34 13.131 16.517 3.629 1.00 9.73 C\nATOM 245 CD1 ILE A 34 10.151 16.024 2.938 1.00 13.41 C\nATOM 246 N ILE A 35 14.856 16.493 6.536 1.00 7.06 N\nATOM 247 CA ILE A 35 15.930 17.454 6.941 1.00 7.52 C\nATOM 248 C ILE A 35 16.913 17.550 5.819 1.00 6.63 C\nATOM 249 O ILE A 35 17.097 16.660 4.970 1.00 7.90 O\nATOM 250 CB ILE A 35 16.622 16.995 8.285 1.00 8.07 C\nATOM 251 CG1 ILE A 35 17.360 15.651 8.067 1.00 9.41 C\nATOM 252 CG2 ILE A 35 15.592 16.974 9.434 1.00 9.46 C\nATOM 253 CD1 ILE A 35 18.298 15.206 9.219 1.00 9.85 C\nATOM 254 N PRO A 36 17.664 18.669 5.806 1.00 8.07 N\nATOM 255 CA PRO A 36 18.635 18.861 4.738 1.00 8.78 C\nATOM 256 C PRO A 36 19.925 18.042 4.949 1.00 8.31 C\nATOM 257 O PRO A 36 20.593 17.742 3.945 1.00 9.09 O\nATOM 258 CB PRO A 36 18.945 20.364 4.783 1.00 9.67 C\nATOM 259 CG PRO A 36 18.238 20.937 5.908 1.00 10.15 C\nATOM 260 CD PRO A 36 17.371 19.900 6.596 1.00 9.53 C\nATOM 261 N GLY A 37 20.172 17.730 6.217 1.00 8.48 N\nATOM 262 CA GLY A 37 21.452 16.969 6.513 1.00 9.20 C\nATOM 263 C GLY A 37 21.143 15.478 6.427 1.00 10.41 C\nATOM 264 O GLY A 37 20.138 15.023 5.878 1.00 12.06 O\nATOM 265 N ALA A 38 22.055 14.701 7.032 1.00 9.24 N\nATOM 266 CA ALA A 38 22.019 13.242 7.020 1.00 9.24 C\nATOM 267 C ALA A 38 21.944 12.628 8.396 1.00 9.60 C\nATOM 268 O ALA A 38 21.869 11.387 8.435 1.00 13.65 O\nATOM 269 CB ALA A 38 23.246 12.697 6.275 1.00 10.43 C\nATOM 270 N THR A 39 21.894 13.435 9.436 1.00 8.70 N\nATOM 271 CA THR A 39 21.936 12.911 10.809 1.00 9.46 C\nATOM 272 C THR A 39 20.615 13.191 11.521 1.00 8.32 C\nATOM 273 O THR A 39 20.357 14.317 11.948 1.00 9.89 O\nATOM 274 CB THR A 39 23.131 13.601 11.593 1.00 10.72 C\nATOM 275 OG1 THR A 39 24.284 13.401 10.709 1.00 11.66 O\nATOM 276 CG2 THR A 39 23.340 12.935 12.962 1.00 11.81 C\nATOM 277 N CYS A 40 19.827 12.110 11.642 1.00 7.64 N\nATOM 278 CA CYS A 40 18.504 12.312 12.298 1.00 8.05 C\nATOM 279 C CYS A 40 18.684 12.451 13.784 1.00 7.63 C\nATOM 280 O CYS A 40 19.533 11.718 14.362 1.00 9.64 O\nATOM 281 CB CYS A 40 17.582 11.117 11.996 1.00 7.80 C\nATOM 282 SG CYS A 40 17.199 10.929 10.237 1.00 7.30 S\nATOM 283 N PRO A 41 17.880 13.266 14.426 1.00 8.00 N\nATOM 284 CA PRO A 41 17.924 13.421 15.877 1.00 8.96 C\nATOM 285 C PRO A 41 17.392 12.206 16.594 1.00 9.06 C\nATOM 286 O PRO A 41 16.652 11.368 16.033 1.00 8.82 O\nATOM 287 CB PRO A 41 17.076 14.658 16.145 1.00 10.39 C\nATOM 288 CG PRO A 41 16.098 14.689 14.997 1.00 10.99 C\nATOM 289 CD PRO A 41 16.859 14.150 13.779 1.00 10.49 C\nATOM 290 N GLY A 42 17.728 12.124 17.884 1.00 7.55 N\nATOM 291 CA GLY A 42 17.334 10.956 18.691 1.00 8.00 C\nATOM 292 C GLY A 42 15.875 10.688 18.871 1.00 7.22 C\nATOM 293 O GLY A 42 15.434 9.550 19.166 1.00 8.41 O\nATOM 294 N ASP A 43 15.036 11.747 18.715 1.00 5.54 N\nATOM 295 CA ASP A 43 13.564 11.573 18.836 1.00 5.85 C\nATOM 296 C ASP A 43 12.936 11.227 17.470 1.00 5.87 C\nATOM 297 O ASP A 43 11.720 11.040 17.428 1.00 7.29 O\nATOM 298 CB ASP A 43 12.933 12.737 19.580 1.00 6.72 C\nATOM 299 CG ASP A 43 13.140 14.094 18.958 1.00 8.59 C\nATOM 300 OD1 ASP A 43 14.109 14.303 18.212 1.00 9.59 O\nATOM 301 OD2 ASP A 43 12.267 14.963 19.265 1.00 11.45 O\nATOM 302 N TYR A 44 13.725 11.174 16.425 1.00 5.22 N\nATOM 303 CA TYR A 44 13.257 10.745 15.081 1.00 5.56 C\nATOM 304 C TYR A 44 14.275 9.687 14.612 1.00 4.61 C\nATOM 305 O TYR A 44 14.930 9.862 13.568 1.00 6.04 O\nATOM 306 CB TYR A 44 13.200 11.914 14.071 1.00 5.41 C\nATOM 307 CG TYR A 44 12.000 12.819 14.399 1.00 5.34 C\nATOM 308 CD1 TYR A 44 12.119 13.853 15.332 1.00 6.59 C\nATOM 309 CD2 TYR A 44 10.775 12.617 13.762 1.00 5.94 C\nATOM 310 CE1 TYR A 44 11.045 14.675 15.610 1.00 5.97 C\nATOM 311 CE2 TYR A 44 9.676 13.433 14.048 1.00 5.17 C\nATOM 312 CZ TYR A 44 9.802 14.456 14.996 1.00 5.96 C\nATOM 313 OH TYR A 44 8.740 15.265 15.269 1.00 8.60 O\nATOM 314 N ALA A 45 14.342 8.640 15.422 1.00 4.76 N\nATOM 315 CA ALA A 45 15.445 7.667 15.246 1.00 5.89 C\nATOM 316 C ALA A 45 15.171 6.533 14.280 1.00 6.67 C\nATOM 317 O ALA A 45 16.093 5.705 14.039 1.00 7.56 O\nATOM 318 CB ALA A 45 15.680 7.099 16.682 1.00 6.82 C\nATOM 319 N ASN A 46 13.966 6.502 13.739 1.00 5.80 N\nATOM 320 CA ASN A 46 13.512 5.395 12.878 1.00 6.15 C\nATOM 321 C ASN A 46 13.311 5.853 11.455 1.00 6.61 C\nATOM 322 O ASN A 46 13.733 6.929 11.026 1.00 7.18 O\nATOM 323 CB ASN A 46 12.266 4.769 13.501 1.00 7.27 C\nATOM 324 CG ASN A 46 12.538 4.304 14.922 1.00 7.98 C\nATOM 325 OD1 ASN A 46 11.982 4.849 15.886 1.00 11.00 O\nATOM 326 ND2 ASN A 46 13.407 3.298 15.015 1.00 10.32 N\nATOM 327 OXT ASN A 46 12.703 4.973 10.746 1.00 7.86 O\nTER 328 ASN A 46\n';Mol2.loadMolecule(ChemDoodle.readPDB(Fmol, 1));Mol2.startAnimation();Mol2.stopAnimation();var resType = 'amino';function setDisp2(obj){Mol2.specs["proteins_display"+obj.value]=obj.checked;Mol2.repaint()}function setProj2(yesPers){Mol2.specs.projectionPerspective_3D=yesPers;Mol2.setupScene();Mol2.repaint()}function setColor2(obj){Mol2.specs.proteins_residueColor=resType=obj.value;Mol2.repaint()}function resColor2(obj){this.checked ? Mol2.specs.proteins_residueColor=resType : Mol2.specs.proteins_residueColor='none';Mol2.repaint()}</script><br><span class="meta">视图: <input type="radio" name="group2" onclick="setProj2(true)">投影 <input type="radio" name="group2" onclick="setProj2(false)" checked="">正交<br>着色: <input type="checkbox" onclick="Mol2.specs.macro_colorByChain=this.checked;Mol2.repaint()">按链 <input type="checkbox" onclick="resColor2(this)">按残基<br>模式: <input type="checkbox" value="Ribbon" checked="" onclick="setDisp2(this)">飘带 <input type="checkbox" value="Backbone" onclick="setDisp2(this)">骨架 <input type="checkbox" value="PipePlank" onclick="setDisp2(this)">管板 <input type="checkbox" checked="" onclick="Mol2.specs.proteins_ribbonCartoonize=this.checked;Mol2.repaint()">卡通<br>显示: <input type="checkbox" onclick="Mol2.specs.macro_showWater=this.checked;Mol2.repaint()">水分子 <input type="checkbox" onclick="Mol2.specs.atoms_nonBondedAsStars_3D=this.checked;Mol2.repaint()">非键原子 <input type="checkbox" onclick="Mol2.specs.atoms_displayLabels_3D=this.checked;Mol2.repaint()">名称<br>颜色: <input type="radio" value="amino" name="radio2" onclick="setColor2(this)">氨基酸 <input type="radio" value="shapely" name="radio2" onclick="setColor2(this)">形状 <input type="radio" value="polarity" name="radio2" onclick="setColor2(this)">极性 <input type="radio" value="acidity" name="radio2" onclick="setColor2(this)">酸性 <input type="radio" value="rainbow" name="radio2" onclick="setColor2(this)">彩虹<br>左键: 转动 滚轮: 缩放 双击: 自动旋转开关 Alt+左键: 移动</span><br><figurecaption>Fig.2</figurecaption></figure>1. 获得标准蛋白的拓扑: pdb2gmx
先将原pdb文件中的20XXX修改为标准残基, 用于定位, 具体改为哪种都可以, 为简单起见, 最好使用GLY或ALA. 对我们要处理的情况, 由于20XXX是由20GLY修饰而来, 所以使用原来的GLY就好了.
变为标准残基蛋白后先对pdb文件进行清理, 设置好两性残基的质子化状态, 然后使用pdb2gmx补充缺失的氢原子, 最后生成AMBER力场的拓扑.
使用对生成的拓扑进行短时间的模拟, 确认拓扑正常.
<div class="highlight"><pre style="line-height:125%"><span></span><span style="color: #008800; font-style: italic">; residue 19 PRO rtp PRO q 0.0</span>
<span style="color: #666666">273</span> N <span style="color: #666666">19</span> PRO N <span style="color: #666666">273</span> <span style="color: #666666">-0.2548</span> <span style="color: #666666">14.01</span>
<span style="color: #666666">274</span> CT <span style="color: #666666">19</span> PRO CD <span style="color: #666666">274</span> <span style="color: #666666">0.0192</span> <span style="color: #666666">12.01</span>
<span style="color: #666666">275</span> H1 <span style="color: #666666">19</span> PRO HD1 <span style="color: #666666">275</span> <span style="color: #666666">0.0391</span> <span style="color: #666666">1.008</span>
<span style="color: #666666">276</span> H1 <span style="color: #666666">19</span> PRO HD2 <span style="color: #666666">276</span> <span style="color: #666666">0.0391</span> <span style="color: #666666">1.008</span>
<span style="color: #666666">277</span> CT <span style="color: #666666">19</span> PRO CG <span style="color: #666666">277</span> <span style="color: #666666">0.0189</span> <span style="color: #666666">12.01</span>
<span style="color: #666666">278</span> HC <span style="color: #666666">19</span> PRO HG1 <span style="color: #666666">278</span> <span style="color: #666666">0.0213</span> <span style="color: #666666">1.008</span>
<span style="color: #666666">279</span> HC <span style="color: #666666">19</span> PRO HG2 <span style="color: #666666">279</span> <span style="color: #666666">0.0213</span> <span style="color: #666666">1.008</span>
<span style="color: #666666">280</span> CT <span style="color: #666666">19</span> PRO CB <span style="color: #666666">280</span> <span style="color: #666666">-0.007</span> <span style="color: #666666">12.01</span>
<span style="color: #666666">281</span> HC <span style="color: #666666">19</span> PRO HB1 <span style="color: #666666">281</span> <span style="color: #666666">0.0253</span> <span style="color: #666666">1.008</span>
<span style="color: #666666">282</span> HC <span style="color: #666666">19</span> PRO HB2 <span style="color: #666666">282</span> <span style="color: #666666">0.0253</span> <span style="color: #666666">1.008</span>
<span style="color: #666666">283</span> CT <span style="color: #666666">19</span> PRO CA <span style="color: #666666">283</span> <span style="color: #666666">-0.0266</span> <span style="color: #666666">12.01</span>
<span style="color: #666666">284</span> H1 <span style="color: #666666">19</span> PRO HA <span style="color: #666666">284</span> <span style="color: #666666">0.0641</span> <span style="color: #666666">1.008</span>
<span style="color: #666666">285</span> C <span style="color: #666666">19</span> PRO C <span style="color: #666666">285</span> <span style="color: #666666">0.5896</span> <span style="color: #666666">12.01</span>
<span style="color: #666666">286</span> O <span style="color: #666666">19</span> PRO O <span style="color: #666666">286</span> <span style="color: #666666">-0.5748</span> <span style="color: #666666">16</span><span style="color: #008800; font-style: italic"> ; qtot 3</span>
<span style="color: #008800; font-style: italic">; residue 20 GLY rtp GLY q 0.0</span>
<span style="color: #666666">287</span> N <span style="color: #666666">20</span> GLY N <span style="color: #666666">287</span> <span style="color: #666666">-0.4157</span> <span style="color: #666666">14.01</span>
<span style="color: #666666">288</span> H <span style="color: #666666">20</span> GLY H <span style="color: #666666">288</span> <span style="color: #666666">0.2719</span> <span style="color: #666666">1.008</span>
<span style="color: #666666">289</span> CT <span style="color: #666666">20</span> GLY CA <span style="color: #666666">289</span> <span style="color: #666666">-0.0252</span> <span style="color: #666666">12.01</span>
<span style="color: #666666">290</span> H1 <span style="color: #666666">20</span> GLY HA1 <span style="color: #666666">290</span> <span style="color: #666666">0.0698</span> <span style="color: #666666">1.008</span>
<span style="color: #666666">291</span> H1 <span style="color: #666666">20</span> GLY HA2 <span style="color: #666666">291</span> <span style="color: #666666">0.0698</span> <span style="color: #666666">1.008</span>
<span style="color: #666666">292</span> C <span style="color: #666666">20</span> GLY C <span style="color: #666666">292</span> <span style="color: #666666">0.5973</span> <span style="color: #666666">12.01</span>
<span style="color: #666666">293</span> O <span style="color: #666666">20</span> GLY O <span style="color: #666666">293</span> <span style="color: #666666">-0.5679</span> <span style="color: #666666">16</span><span style="color: #008800; font-style: italic"> ; qtot 3</span>
<span style="color: #008800; font-style: italic">; residue 21 THR rtp THR q 0.0</span>
<span style="color: #666666">294</span> N <span style="color: #666666">21</span> THR N <span style="color: #666666">294</span> <span style="color: #666666">-0.4157</span> <span style="color: #666666">14.01</span>
<span style="color: #666666">295</span> H <span style="color: #666666">21</span> THR H <span style="color: #666666">295</span> <span style="color: #666666">0.2719</span> <span style="color: #666666">1.008</span>
<span style="color: #666666">296</span> CT <span style="color: #666666">21</span> THR CA <span style="color: #666666">296</span> <span style="color: #666666">-0.0389</span> <span style="color: #666666">12.01</span>
<span style="color: #666666">297</span> H1 <span style="color: #666666">21</span> THR HA <span style="color: #666666">297</span> <span style="color: #666666">0.1007</span> <span style="color: #666666">1.008</span>
<span style="color: #666666">298</span> CT <span style="color: #666666">21</span> THR CB <span style="color: #666666">298</span> <span style="color: #666666">0.3654</span> <span style="color: #666666">12.01</span>
<span style="color: #666666">299</span> H1 <span style="color: #666666">21</span> THR HB <span style="color: #666666">299</span> <span style="color: #666666">0.0043</span> <span style="color: #666666">1.008</span>
<span style="color: #666666">300</span> CT <span style="color: #666666">21</span> THR CG2 <span style="color: #666666">300</span> <span style="color: #666666">-0.2438</span> <span style="color: #666666">12.01</span>
<span style="color: #666666">301</span> HC <span style="color: #666666">21</span> THR HG21 <span style="color: #666666">301</span> <span style="color: #666666">0.0642</span> <span style="color: #666666">1.008</span>
<span style="color: #666666">302</span> HC <span style="color: #666666">21</span> THR HG22 <span style="color: #666666">302</span> <span style="color: #666666">0.0642</span> <span style="color: #666666">1.008</span>
<span style="color: #666666">303</span> HC <span style="color: #666666">21</span> THR HG23 <span style="color: #666666">303</span> <span style="color: #666666">0.0642</span> <span style="color: #666666">1.008</span>
<span style="color: #666666">304</span> OH <span style="color: #666666">21</span> THR OG1 <span style="color: #666666">304</span> <span style="color: #666666">-0.6761</span> <span style="color: #666666">16</span>
<span style="color: #666666">305</span> HO <span style="color: #666666">21</span> THR HG1 <span style="color: #666666">305</span> <span style="color: #666666">0.4102</span> <span style="color: #666666">1.008</span>
<span style="color: #666666">306</span> C <span style="color: #666666">21</span> THR C <span style="color: #666666">306</span> <span style="color: #666666">0.5973</span> <span style="color: #666666">12.01</span>
<span style="color: #666666">307</span> O <span style="color: #666666">21</span> THR O <span style="color: #666666">307</span> <span style="color: #666666">-0.5679</span> <span style="color: #666666">16</span><span style="color: #008800; font-style: italic"> ; qtot 3</span></pre></div>检查生成的拓扑文件和构型文件, 发现补充完整后蛋白的总原子数为642, 其中19PRO的原子编号从273开始, 20GLY的编号范围为287:293, 21THR从294开始. 记下这些数字, 后面会用到.
2. 删除蛋白拓扑中用于定位非标准残基的标准残基: 2-2_删除top原子.js
由于我们要使用20XXX替换原本的20GLY, 所以先将20GLY的所有原子及其参与的成键项删除. 为此, 选中拓扑中[ atoms ]到[ dihedrals ]的内容, 然后启动脚本2-2_删除top原子.js
可以直接使用所得结果替换原先选中内容. 如果还不熟悉整个流程, 可以另存为一个文件, 以便与原拓扑对比. 熟悉流程之后, 直接在原文件上修改即可.
与原始拓扑对比一下, 可以发现[ atoms ]中20GLY对应的原子已经删除了.
<div class="highlight"><pre style="line-height:125%"><span></span><span style="color: #008800; font-style: italic">; residue 19 PRO rtp PRO q 0.0</span>
<span style="color: #666666">273</span> N <span style="color: #666666">19</span> PRO N <span style="color: #666666">273</span> <span style="color: #666666">-0.2548</span> <span style="color: #666666">14.01</span>
<span style="color: #666666">274</span> CT <span style="color: #666666">19</span> PRO CD <span style="color: #666666">274</span> <span style="color: #666666">0.0192</span> <span style="color: #666666">12.01</span>
<span style="color: #666666">275</span> H1 <span style="color: #666666">19</span> PRO HD1 <span style="color: #666666">275</span> <span style="color: #666666">0.0391</span> <span style="color: #666666">1.008</span>
<span style="color: #666666">276</span> H1 <span style="color: #666666">19</span> PRO HD2 <span style="color: #666666">276</span> <span style="color: #666666">0.0391</span> <span style="color: #666666">1.008</span>
<span style="color: #666666">277</span> CT <span style="color: #666666">19</span> PRO CG <span style="color: #666666">277</span> <span style="color: #666666">0.0189</span> <span style="color: #666666">12.01</span>
<span style="color: #666666">278</span> HC <span style="color: #666666">19</span> PRO HG1 <span style="color: #666666">278</span> <span style="color: #666666">0.0213</span> <span style="color: #666666">1.008</span>
<span style="color: #666666">279</span> HC <span style="color: #666666">19</span> PRO HG2 <span style="color: #666666">279</span> <span style="color: #666666">0.0213</span> <span style="color: #666666">1.008</span>
<span style="color: #666666">280</span> CT <span style="color: #666666">19</span> PRO CB <span style="color: #666666">280</span> <span style="color: #666666">-0.007</span> <span style="color: #666666">12.01</span>
<span style="color: #666666">281</span> HC <span style="color: #666666">19</span> PRO HB1 <span style="color: #666666">281</span> <span style="color: #666666">0.0253</span> <span style="color: #666666">1.008</span>
<span style="color: #666666">282</span> HC <span style="color: #666666">19</span> PRO HB2 <span style="color: #666666">282</span> <span style="color: #666666">0.0253</span> <span style="color: #666666">1.008</span>
<span style="color: #666666">283</span> CT <span style="color: #666666">19</span> PRO CA <span style="color: #666666">283</span> <span style="color: #666666">-0.0266</span> <span style="color: #666666">12.01</span>
<span style="color: #666666">284</span> H1 <span style="color: #666666">19</span> PRO HA <span style="color: #666666">284</span> <span style="color: #666666">0.0641</span> <span style="color: #666666">1.008</span>
<span style="color: #666666">285</span> C <span style="color: #666666">19</span> PRO C <span style="color: #666666">285</span> <span style="color: #666666">0.5896</span> <span style="color: #666666">12.01</span>
<span style="color: #666666">286</span> O <span style="color: #666666">19</span> PRO O <span style="color: #666666">286</span> <span style="color: #666666">-0.5748</span> <span style="color: #666666">16</span><span style="color: #008800; font-style: italic"> ; qtot 3</span>
<span style="color: #008800; font-style: italic">; residue 20 GLY rtp GLY q 0.0</span>
<span style="color: #008800; font-style: italic">; residue 21 THR rtp THR q 0.0</span>
<span style="color: #666666">294</span> N <span style="color: #666666">21</span> THR N <span style="color: #666666">294</span> <span style="color: #666666">-0.4157</span> <span style="color: #666666">14.01</span>
<span style="color: #666666">295</span> H <span style="color: #666666">21</span> THR H <span style="color: #666666">295</span> <span style="color: #666666">0.2719</span> <span style="color: #666666">1.008</span>
<span style="color: #666666">296</span> CT <span style="color: #666666">21</span> THR CA <span style="color: #666666">296</span> <span style="color: #666666">-0.0389</span> <span style="color: #666666">12.01</span>
<span style="color: #666666">297</span> H1 <span style="color: #666666">21</span> THR HA <span style="color: #666666">297</span> <span style="color: #666666">0.1007</span> <span style="color: #666666">1.008</span>
<span style="color: #666666">298</span> CT <span style="color: #666666">21</span> THR CB <span style="color: #666666">298</span> <span style="color: #666666">0.3654</span> <span style="color: #666666">12.01</span>
<span style="color: #666666">299</span> H1 <span style="color: #666666">21</span> THR HB <span style="color: #666666">299</span> <span style="color: #666666">0.0043</span> <span style="color: #666666">1.008</span>
<span style="color: #666666">300</span> CT <span style="color: #666666">21</span> THR CG2 <span style="color: #666666">300</span> <span style="color: #666666">-0.2438</span> <span style="color: #666666">12.01</span>
<span style="color: #666666">301</span> HC <span style="color: #666666">21</span> THR HG21 <span style="color: #666666">301</span> <span style="color: #666666">0.0642</span> <span style="color: #666666">1.008</span>
<span style="color: #666666">302</span> HC <span style="color: #666666">21</span> THR HG22 <span style="color: #666666">302</span> <span style="color: #666666">0.0642</span> <span style="color: #666666">1.008</span>
<span style="color: #666666">303</span> HC <span style="color: #666666">21</span> THR HG23 <span style="color: #666666">303</span> <span style="color: #666666">0.0642</span> <span style="color: #666666">1.008</span>
<span style="color: #666666">304</span> OH <span style="color: #666666">21</span> THR OG1 <span style="color: #666666">304</span> <span style="color: #666666">-0.6761</span> <span style="color: #666666">16</span>
<span style="color: #666666">305</span> HO <span style="color: #666666">21</span> THR HG1 <span style="color: #666666">305</span> <span style="color: #666666">0.4102</span> <span style="color: #666666">1.008</span>
<span style="color: #666666">306</span> C <span style="color: #666666">21</span> THR C <span style="color: #666666">306</span> <span style="color: #666666">0.5973</span> <span style="color: #666666">12.01</span>
<span style="color: #666666">307</span> O <span style="color: #666666">21</span> THR O <span style="color: #666666">307</span> <span style="color: #666666">-0.5679</span> <span style="color: #666666">16</span><span style="color: #008800; font-style: italic"> ; qtot 3</span></pre></div>此外, 后面所有涉及20GLY原子的成键项也已经删除.
3. 调整蛋白拓扑的原子编号, 留出非标准残基的位置: 2-1_调整top原子编号.js
20XXX的拓扑最终要合并到蛋白拓扑中, 所以必须先在蛋白拓扑中为其预留下位置, 也就是要调整蛋白拓扑的原子编号, 使其与最终拓扑中的一致.
20XXX共38个原子, 所以蛋白拓扑中要空出38个位置. 因此, 从21THR的第一个原子N294开始, 后续所有原子编号都要进行修改, 294要变为286+38+1=325. 为此, 我们像上一步一样, 选中拓扑中的原子及成键项, 然后启动脚本2-1_调整top原子编号.js
因为我们要修改N294及其后面所有原子的编号, 所以终止编号足够大即可.
将所得结果替换原先选中内容, 就得到了所需的蛋白拓扑.
<div class="highlight"><pre style="line-height:125%"><span></span><span style="color: #008800; font-style: italic">; residue 19 PRO rtp PRO q 0.0</span>
<span style="color: #666666">273</span> N <span style="color: #666666">19</span> PRO N <span style="color: #666666">273</span> <span style="color: #666666">-0.2548</span> <span style="color: #666666">14.01</span>
<span style="color: #666666">274</span> CT <span style="color: #666666">19</span> PRO CD <span style="color: #666666">274</span> <span style="color: #666666">0.0192</span> <span style="color: #666666">12.01</span>
<span style="color: #666666">275</span> H1 <span style="color: #666666">19</span> PRO HD1 <span style="color: #666666">275</span> <span style="color: #666666">0.0391</span> <span style="color: #666666">1.008</span>
<span style="color: #666666">276</span> H1 <span style="color: #666666">19</span> PRO HD2 <span style="color: #666666">276</span> <span style="color: #666666">0.0391</span> <span style="color: #666666">1.008</span>
<span style="color: #666666">277</span> CT <span style="color: #666666">19</span> PRO CG <span style="color: #666666">277</span> <span style="color: #666666">0.0189</span> <span style="color: #666666">12.01</span>
<span style="color: #666666">278</span> HC <span style="color: #666666">19</span> PRO HG1 <span style="color: #666666">278</span> <span style="color: #666666">0.0213</span> <span style="color: #666666">1.008</span>
<span style="color: #666666">279</span> HC <span style="color: #666666">19</span> PRO HG2 <span style="color: #666666">279</span> <span style="color: #666666">0.0213</span> <span style="color: #666666">1.008</span>
<span style="color: #666666">280</span> CT <span style="color: #666666">19</span> PRO CB <span style="color: #666666">280</span> <span style="color: #666666">-0.007</span> <span style="color: #666666">12.01</span>
<span style="color: #666666">281</span> HC <span style="color: #666666">19</span> PRO HB1 <span style="color: #666666">281</span> <span style="color: #666666">0.0253</span> <span style="color: #666666">1.008</span>
<span style="color: #666666">282</span> HC <span style="color: #666666">19</span> PRO HB2 <span style="color: #666666">282</span> <span style="color: #666666">0.0253</span> <span style="color: #666666">1.008</span>
<span style="color: #666666">283</span> CT <span style="color: #666666">19</span> PRO CA <span style="color: #666666">283</span> <span style="color: #666666">-0.0266</span> <span style="color: #666666">12.01</span>
<span style="color: #666666">284</span> H1 <span style="color: #666666">19</span> PRO HA <span style="color: #666666">284</span> <span style="color: #666666">0.0641</span> <span style="color: #666666">1.008</span>
<span style="color: #666666">285</span> C <span style="color: #666666">19</span> PRO C <span style="color: #666666">285</span> <span style="color: #666666">0.5896</span> <span style="color: #666666">12.01</span>
<span style="color: #666666">286</span> O <span style="color: #666666">19</span> PRO O <span style="color: #666666">286</span> <span style="color: #666666">-0.5748</span> <span style="color: #666666">16</span><span style="color: #008800; font-style: italic"> ; qtot 3</span>
<span style="color: #008800; font-style: italic">; residue 20 GLY rtp GLY q 0.0</span>
<span style="color: #008800; font-style: italic">; residue 21 THR rtp THR q 0.0</span>
<span style="color: #666666">325</span> N <span style="color: #666666">21</span> THR N <span style="color: #666666">294</span> <span style="color: #666666">-0.4157</span> <span style="color: #666666">14.01</span>
<span style="color: #666666">326</span> H <span style="color: #666666">21</span> THR H <span style="color: #666666">295</span> <span style="color: #666666">0.2719</span> <span style="color: #666666">1.008</span>
<span style="color: #666666">327</span> CT <span style="color: #666666">21</span> THR CA <span style="color: #666666">296</span> <span style="color: #666666">-0.0389</span> <span style="color: #666666">12.01</span>
<span style="color: #666666">328</span> H1 <span style="color: #666666">21</span> THR HA <span style="color: #666666">297</span> <span style="color: #666666">0.1007</span> <span style="color: #666666">1.008</span>
<span style="color: #666666">329</span> CT <span style="color: #666666">21</span> THR CB <span style="color: #666666">298</span> <span style="color: #666666">0.3654</span> <span style="color: #666666">12.01</span>
<span style="color: #666666">330</span> H1 <span style="color: #666666">21</span> THR HB <span style="color: #666666">299</span> <span style="color: #666666">0.0043</span> <span style="color: #666666">1.008</span>
<span style="color: #666666">331</span> CT <span style="color: #666666">21</span> THR CG2 <span style="color: #666666">300</span> <span style="color: #666666">-0.2438</span> <span style="color: #666666">12.01</span>
<span style="color: #666666">332</span> HC <span style="color: #666666">21</span> THR HG21 <span style="color: #666666">301</span> <span style="color: #666666">0.0642</span> <span style="color: #666666">1.008</span>
<span style="color: #666666">333</span> HC <span style="color: #666666">21</span> THR HG22 <span style="color: #666666">302</span> <span style="color: #666666">0.0642</span> <span style="color: #666666">1.008</span>
<span style="color: #666666">334</span> HC <span style="color: #666666">21</span> THR HG23 <span style="color: #666666">303</span> <span style="color: #666666">0.0642</span> <span style="color: #666666">1.008</span>
<span style="color: #666666">335</span> OH <span style="color: #666666">21</span> THR OG1 <span style="color: #666666">304</span> <span style="color: #666666">-0.6761</span> <span style="color: #666666">16</span>
<span style="color: #666666">336</span> HO <span style="color: #666666">21</span> THR HG1 <span style="color: #666666">305</span> <span style="color: #666666">0.4102</span> <span style="color: #666666">1.008</span>
<span style="color: #666666">337</span> C <span style="color: #666666">21</span> THR C <span style="color: #666666">306</span> <span style="color: #666666">0.5973</span> <span style="color: #666666">12.01</span>
<span style="color: #666666">338</span> O <span style="color: #666666">21</span> THR O <span style="color: #666666">307</span> <span style="color: #666666">-0.5679</span> <span style="color: #666666">16</span><span style="color: #008800; font-style: italic"> ; qtot 3</span></pre></div>对比检查一下, 确认原子及成键项的编号调整正确.
这样我们就处理好了蛋白部分的拓扑, 等着补充暂时缺失的20XXX拓扑及其成键项.
4. 抽取非标准残基及其两端所连残基, 封端, 获取其GAFF拓扑: ambertools
现在开始处理20XXX. 它处于肽链之中, 前后与其他残基相连, 以常用的NC端顺序而言, 其前端与19PRO的C端相连, 其后端与21THR的N端相连. 我们先将19PRO, 20XXX, 21THR三个残基从PDB中抽取出来
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var Fmol='66\nlig\nN 3.330 4.790 -4.540\nC 2.420 4.940 -3.410\nH 2.870 5.460 -2.680\nH 2.160 4.040 -3.060\nC 1.220 5.690 -3.990\nH 1.190 6.620 -3.630\nH 0.370 5.220 -3.770\nC 1.360 5.770 -5.470\nH 1.170 6.700 -5.780\nH 0.710 5.130 -5.900\nC 2.790 5.380 -5.800\nH 2.870 4.700 -6.530\nC 3.570 6.540 -6.320\nO 3.260 7.050 -7.420\nN 4.560 7.050 -5.560\nH 4.760 6.640 -4.670\nC 5.370 8.190 -6.020\nH 6.330 7.970 -5.860\nC 5.010 9.480 -5.280\nO 5.530 10.510 -5.730\nC 4.803 9.870 -11.977\nC 5.547 9.942 -13.162\nC 6.945 10.028 -13.109\nC 7.599 10.043 -11.869\nC 6.855 9.971 -10.684\nC 5.457 9.884 -10.737\nH 3.736 9.804 -12.018\nH 5.048 9.931 -14.109\nH 8.666 10.108 -11.828\nH 7.355 9.983 -9.738\nC 7.762 10.107 -14.412\nH 7.181 10.592 -15.168\nC 9.052 10.911 -14.161\nH 9.620 10.965 -15.066\nH 8.799 11.899 -13.838\nH 9.633 10.425 -13.405\nC 8.125 8.685 -14.877\nO 9.186 8.486 -15.523\nO 7.257 7.590 -14.574\nH 7.773 6.785 -14.489\nC 4.640 9.805 -9.435\nC 5.476 9.108 -8.346\nC 5.840 7.685 -8.811\nH 6.372 9.666 -8.171\nH 4.944 7.127 -8.985\nH 6.407 7.740 -9.716\nH 6.420 7.199 -8.055\nC 4.660 9.028 -7.043\nH 4.406 10.017 -6.720\nH 3.763 8.470 -7.218\nH 3.744 9.247 -9.609\nH 4.388 10.793 -9.112\nN 4.180 9.440 -4.260\nH 3.820 8.550 -3.990\nC 3.770 10.610 -3.510\nH 3.200 11.120 -4.160\nC 2.990 10.190 -2.220\nH 3.610 9.820 -1.530\nC 2.260 11.350 -1.550\nH 1.790 11.020 -0.740\nH 2.920 12.050 -1.290\nH 1.590 11.740 -2.190\nO 2.050 9.140 -2.620\nH 1.530 8.840 -1.820\nC 5.020 11.400 -3.040\nO 5.950 10.760 -2.520\n';molxyz=ChemDoodle.readXYZ(Fmol)
Mol3.loadMolecule(ChemDoodle.readXYZ(Fmol));
Mol3.startAnimation();Mol3.stopAnimation();function setProj3(yesPers){Mol3.specs.projectionPerspective_3D=yesPers;Mol3.setupScene();Mol3.repaint()}function setModel3(model){Mol3.specs.set3DRepresentation(model);Mol3.setupScene();Mol3.repaint()}function setSpeed3(){Mol3.timeout=500-document.getElementById('spd3').value;Mol3.loadMolecule(ChemDoodle.readXYZ(Fmol));
Mol3.startAnimation()}</script><br><span class='meta'>视图: <input type='radio' name='group2' onclick='setProj3(true)'>投影 <input type='radio' name='group2' onclick='setProj3(false)' checked=''>正交 速度: <input type='range' id='spd3' min='1' max='500' onchange='setSpeed3()'/><br>模型: <input type='radio' name='model' onclick='setModel3('Ball and Stick')' checked=''>球棍 <input type='radio' name='model' onclick='setModel3('van der Waals Spheres')'>范德华球 <input type='radio' name='model' onclick='setModel3('Stick')'>棍状 <input type='radio' name='model' onclick='setModel3('Wireframe')'>线框 <input type='radio' name='model' onclick='setModel3('Line')'>线型 <input type='checkbox' onclick='Mol3.specs.atoms_displayLabels_3D=this.checked;Mol3.repaint()'>名称<br>左键: 转动 滚轮: 缩放 双击: 自动旋转开关 Alt+左键: 移动</span><br><figurecaption>Fig.3</figurecaption></figure>这里之所以不只使用20XXX, 是因为后面将20XXX的拓扑补充到蛋白拓扑中时, 会涉及20XXX与19PRO, 21THR的成键项. 如果只使用20XXX, 有些相应的成键项参数我们要自己补充, 很麻烦, 而使用了前后残基的话, 所有成键参数很容易得到, 后面只要简单复制到蛋白拓扑中就好了.
蛋白我们用了AMBER力场, 非标准残基我们可以使用GAFF力场. 要获得GAFF拓扑首先必须保证分子完整, 也就是要对截取的分子进行封端. 封端的原则是尽量保证其末端原子的化学环境与实际分子中的情况接近. 对于蛋白, 一般是将与C端相连的位置用ACE(-COCH3)封端, 与N端相连位置用NME(-NHCH3)封端.
使用熟悉的分子编辑软件进行封端. 为了后面处理方便, 建议调整一下封端基团的位置, 将ACE放在最前面, NME放在最后面, 也就是按ACE, 19PRO, 20XXX, 21THR, NME的顺序排列原子. 也要注意, 19PRO和21THR自身的原子排列顺序要和前面蛋白中的一致, 否则后面没法保证添加的成键项编号一致.
封端后, 在创建GAFF拓扑前, 一般要使用分子编辑软件进行简单的优化, 使得初始结构尽量合理.
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var Fmol='78\ncap\nC 4.639 4.128 -4.448\nO 5.551 4.681 -3.937\nC 4.701 2.747 -5.038\nH 3.975 2.108 -4.541\nH 4.429 2.789 -6.089\nH 5.695 2.334 -4.928\nN 3.330 4.790 -4.540\nC 2.420 4.940 -3.410\nH 2.870 5.460 -2.680\nH 2.160 4.040 -3.060\nC 1.220 5.690 -3.990\nH 1.190 6.620 -3.630\nH 0.370 5.220 -3.770\nC 1.360 5.770 -5.470\nH 1.170 6.700 -5.780\nH 0.710 5.130 -5.900\nC 2.790 5.380 -5.800\nH 2.870 4.700 -6.530\nC 3.570 6.540 -6.320\nO 3.260 7.050 -7.420\nN 4.560 7.050 -5.560\nH 4.760 6.640 -4.670\nC 5.370 8.190 -6.020\nH 6.330 7.970 -5.860\nC 5.010 9.480 -5.280\nO 5.530 10.510 -5.730\nC 4.803 9.870 -11.977\nC 5.547 9.942 -13.162\nC 6.945 10.028 -13.109\nC 7.599 10.043 -11.869\nC 6.855 9.971 -10.684\nC 5.457 9.884 -10.737\nH 3.736 9.804 -12.018\nH 5.048 9.931 -14.109\nH 8.666 10.108 -11.828\nH 7.355 9.983 -9.738\nC 7.762 10.107 -14.412\nH 7.181 10.592 -15.168\nC 9.052 10.911 -14.161\nH 9.620 10.965 -15.066\nH 8.799 11.899 -13.838\nH 9.633 10.425 -13.405\nC 8.125 8.685 -14.877\nO 9.186 8.486 -15.523\nO 7.257 7.590 -14.574\nH 7.773 6.785 -14.489\nC 4.640 9.805 -9.435\nC 5.476 9.108 -8.346\nC 5.840 7.685 -8.811\nH 6.372 9.666 -8.171\nH 4.944 7.127 -8.985\nH 6.407 7.740 -9.716\nH 6.420 7.199 -8.055\nC 4.660 9.028 -7.043\nH 4.406 10.017 -6.720\nH 3.763 8.470 -7.218\nH 3.744 9.247 -9.609\nH 4.388 10.793 -9.112\nN 4.180 9.440 -4.260\nH 3.820 8.550 -3.990\nC 3.770 10.610 -3.510\nH 3.200 11.120 -4.160\nC 2.990 10.190 -2.220\nH 3.610 9.820 -1.530\nC 2.260 11.350 -1.550\nH 1.790 11.020 -0.740\nH 2.920 12.050 -1.290\nH 1.590 11.740 -2.190\nO 2.050 9.140 -2.620\nH 1.530 8.840 -1.820\nC 5.020 11.400 -3.040\nO 5.985 10.792 -2.508\nN 5.077 12.858 -3.216\nC 5.559 13.503 -2.005\nH 5.697 13.035 -3.980\nH 4.867 13.306 -1.193\nH 5.583 14.577 -2.154\nH 6.553 13.185 -1.684\n';molxyz=ChemDoodle.readXYZ(Fmol)
Mol4.loadMolecule(ChemDoodle.readXYZ(Fmol));
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Mol4.startAnimation()}</script><br><span class='meta'>视图: <input type='radio' name='group2' onclick='setProj4(true)'>投影 <input type='radio' name='group2' onclick='setProj4(false)' checked=''>正交 速度: <input type='range' id='spd4' min='1' max='500' onchange='setSpeed4()'/><br>模型: <input type='radio' name='model' onclick='setModel4('Ball and Stick')' checked=''>球棍 <input type='radio' name='model' onclick='setModel4('van der Waals Spheres')'>范德华球 <input type='radio' name='model' onclick='setModel4('Stick')'>棍状 <input type='radio' name='model' onclick='setModel4('Wireframe')'>线框 <input type='radio' name='model' onclick='setModel4('Line')'>线型 <input type='checkbox' onclick='Mol4.specs.atoms_displayLabels_3D=this.checked;Mol4.repaint()'>名称<br>左键: 转动 滚轮: 缩放 双击: 自动旋转开关 Alt+左键: 移动</span><br><figurecaption>Fig.4</figurecaption></figure>后文我们称这个分子为LIG.
接下来获得LIG分子的GAFF拓扑, 作为测试, 用AM1-BCC电荷就够了. 如果使用RESP电荷, 可以参考我的另一篇教程使用AmberTools+ACPYPE+Gaussian创建小分子GAFF力场的拓扑文件.
可以运行短时间的MD简单测试下所得的GAFF拓扑, 看是否存在问题.
5. 修正非标准残基的电荷
一般情况下, 每个残基的净电荷都是整数, 不带电的残基净电荷是零. 20XXX整体不带电, 所以其38个原子所带电荷之和必须为零, 但由于LIG分子中含有前后残基和封端基团, GAFF只能保证所有原子的净电荷正确, 无法保证20XXX的总电荷为零, 所以必须对20XXX原子的电荷进行修正.
修正的方法很基本, ACE, 19PRO各自的总电荷应该接近零, 21THR, NME各自的总电荷也应该接近零, 所以, 将ACE+19PRO, 21THR+NME从拓扑中删除后, 它们各自的总电荷要想办法分配到20XXX的原子上. 分配的方法也有多种, 既可以直接分配到连接原子上, 也可以平均分配到所有原子上.
查看LIG拓扑的原子部分
<div class="highlight"><pre style="line-height:125%"><span></span>[ atoms ]<span style="color: #008800; font-style: italic"></span>
<span style="color: #008800; font-style: italic">; nr type resi res atom cgnr charge mass ; qtot bond_type</span>
<span style="color: #666666">1</span> c <span style="color: #666666">1</span> lig C <span style="color: #666666">1</span> <span style="color: #666666">0.654097</span> <span style="color: #666666">12.01000</span><span style="color: #008800; font-style: italic"> ; qtot 0.654</span>
<span style="color: #666666">2</span> o <span style="color: #666666">1</span> lig O <span style="color: #666666">2</span> <span style="color: #666666">-0.588101</span> <span style="color: #666666">16.00000</span><span style="color: #008800; font-style: italic"> ; qtot 0.066</span>
<span style="color: #666666">3</span> c3 <span style="color: #666666">1</span> lig C1 <span style="color: #666666">3</span> <span style="color: #666666">-0.175100</span> <span style="color: #666666">12.01000</span><span style="color: #008800; font-style: italic"> ; qtot -0.109</span>
<span style="color: #666666">4</span> hc <span style="color: #666666">1</span> lig H <span style="color: #666666">4</span> <span style="color: #666666">0.072700</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.036</span>
<span style="color: #666666">5</span> hc <span style="color: #666666">1</span> lig H1 <span style="color: #666666">5</span> <span style="color: #666666">0.072700</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot 0.036</span>
<span style="color: #666666">6</span> hc <span style="color: #666666">1</span> lig H2 <span style="color: #666666">6</span> <span style="color: #666666">0.072700</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; ACE qtot 0.109</span>
<span style="color: #666666">7</span> n <span style="color: #666666">1</span> lig N <span style="color: #666666">7</span> <span style="color: #666666">-0.475800</span> <span style="color: #666666">14.01000</span><span style="color: #008800; font-style: italic"> ; qtot -0.367</span>
<span style="color: #666666">8</span> c3 <span style="color: #666666">1</span> lig C2 <span style="color: #666666">8</span> <span style="color: #666666">0.078000</span> <span style="color: #666666">12.01000</span><span style="color: #008800; font-style: italic"> ; qtot -0.289</span>
<span style="color: #666666">9</span> h1 <span style="color: #666666">1</span> lig H3 <span style="color: #666666">9</span> <span style="color: #666666">0.062700</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.226</span>
<span style="color: #666666">10</span> h1 <span style="color: #666666">1</span> lig H4 <span style="color: #666666">10</span> <span style="color: #666666">0.062700</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.163</span>
<span style="color: #666666">11</span> c3 <span style="color: #666666">1</span> lig C3 <span style="color: #666666">11</span> <span style="color: #666666">-0.099400</span> <span style="color: #666666">12.01000</span><span style="color: #008800; font-style: italic"> ; qtot -0.263</span>
<span style="color: #666666">12</span> hc <span style="color: #666666">1</span> lig H5 <span style="color: #666666">12</span> <span style="color: #666666">0.058200</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.205</span>
<span style="color: #666666">13</span> hc <span style="color: #666666">1</span> lig H6 <span style="color: #666666">13</span> <span style="color: #666666">0.058200</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.146</span>
<span style="color: #666666">14</span> c3 <span style="color: #666666">1</span> lig C4 <span style="color: #666666">14</span> <span style="color: #666666">-0.090400</span> <span style="color: #666666">12.01000</span><span style="color: #008800; font-style: italic"> ; qtot -0.237</span>
<span style="color: #666666">15</span> hc <span style="color: #666666">1</span> lig H7 <span style="color: #666666">15</span> <span style="color: #666666">0.067200</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.170</span>
<span style="color: #666666">16</span> hc <span style="color: #666666">1</span> lig H8 <span style="color: #666666">16</span> <span style="color: #666666">0.067200</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.102</span>
<span style="color: #666666">17</span> c3 <span style="color: #666666">1</span> lig C5 <span style="color: #666666">17</span> <span style="color: #666666">0.025700</span> <span style="color: #666666">12.01000</span><span style="color: #008800; font-style: italic"> ; qtot -0.077</span>
<span style="color: #666666">18</span> h1 <span style="color: #666666">1</span> lig H9 <span style="color: #666666">18</span> <span style="color: #666666">0.088700</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot 0.012</span>
<span style="color: #666666">19</span> c <span style="color: #666666">1</span> lig C6 <span style="color: #666666">19</span> <span style="color: #666666">0.656101</span> <span style="color: #666666">12.01000</span><span style="color: #008800; font-style: italic"> ; qtot 0.668</span>
<span style="color: #666666">20</span> o <span style="color: #666666">1</span> lig O1 <span style="color: #666666">20</span> <span style="color: #666666">-0.624101</span> <span style="color: #666666">16.00000</span><span style="color: #008800; font-style: italic"> ; PRO qtot 0.044</span>
<span style="color: #666666">21</span> n <span style="color: #666666">1</span> lig N1 <span style="color: #666666">21</span> <span style="color: #666666">-0.551901</span> <span style="color: #666666">14.01000</span><span style="color: #008800; font-style: italic"> ; qtot -0.508</span>
<span style="color: #666666">22</span> hn <span style="color: #666666">1</span> lig H10 <span style="color: #666666">22</span> <span style="color: #666666">0.328500</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.179</span>
<span style="color: #666666">23</span> c3 <span style="color: #666666">1</span> lig C7 <span style="color: #666666">23</span> <span style="color: #666666">0.050700</span> <span style="color: #666666">12.01000</span><span style="color: #008800; font-style: italic"> ; qtot -0.129</span>
<span style="color: #666666">24</span> h1 <span style="color: #666666">1</span> lig H11 <span style="color: #666666">24</span> <span style="color: #666666">0.088700</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.040</span>
<span style="color: #666666">25</span> c <span style="color: #666666">1</span> lig C8 <span style="color: #666666">25</span> <span style="color: #666666">0.640101</span> <span style="color: #666666">12.01000</span><span style="color: #008800; font-style: italic"> ; qtot 0.600</span>
<span style="color: #666666">26</span> o <span style="color: #666666">1</span> lig O2 <span style="color: #666666">26</span> <span style="color: #666666">-0.639101</span> <span style="color: #666666">16.00000</span><span style="color: #008800; font-style: italic"> ; qtot -0.039</span>
<span style="color: #666666">27</span> ca <span style="color: #666666">1</span> lig C9 <span style="color: #666666">27</span> <span style="color: #666666">-0.129000</span> <span style="color: #666666">12.01000</span><span style="color: #008800; font-style: italic"> ; qtot -0.168</span>
<span style="color: #666666">28</span> ca <span style="color: #666666">1</span> lig C10 <span style="color: #666666">28</span> <span style="color: #666666">-0.112000</span> <span style="color: #666666">12.01000</span><span style="color: #008800; font-style: italic"> ; qtot -0.280</span>
<span style="color: #666666">29</span> ca <span style="color: #666666">1</span> lig C11 <span style="color: #666666">29</span> <span style="color: #666666">-0.095300</span> <span style="color: #666666">12.01000</span><span style="color: #008800; font-style: italic"> ; qtot -0.375</span>
<span style="color: #666666">30</span> ca <span style="color: #666666">1</span> lig C12 <span style="color: #666666">30</span> <span style="color: #666666">-0.112000</span> <span style="color: #666666">12.01000</span><span style="color: #008800; font-style: italic"> ; qtot -0.487</span>
<span style="color: #666666">31</span> ca <span style="color: #666666">1</span> lig C13 <span style="color: #666666">31</span> <span style="color: #666666">-0.129000</span> <span style="color: #666666">12.01000</span><span style="color: #008800; font-style: italic"> ; qtot -0.616</span>
<span style="color: #666666">32</span> ca <span style="color: #666666">1</span> lig C14 <span style="color: #666666">32</span> <span style="color: #666666">-0.069300</span> <span style="color: #666666">12.01000</span><span style="color: #008800; font-style: italic"> ; qtot -0.686</span>
<span style="color: #666666">33</span> ha <span style="color: #666666">1</span> lig H12 <span style="color: #666666">33</span> <span style="color: #666666">0.133000</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.553</span>
<span style="color: #666666">34</span> ha <span style="color: #666666">1</span> lig H13 <span style="color: #666666">34</span> <span style="color: #666666">0.144000</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.409</span>
<span style="color: #666666">35</span> ha <span style="color: #666666">1</span> lig H14 <span style="color: #666666">35</span> <span style="color: #666666">0.144000</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.265</span>
<span style="color: #666666">36</span> ha <span style="color: #666666">1</span> lig H15 <span style="color: #666666">36</span> <span style="color: #666666">0.133000</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.132</span>
<span style="color: #666666">37</span> c3 <span style="color: #666666">1</span> lig C15 <span style="color: #666666">37</span> <span style="color: #666666">-0.056400</span> <span style="color: #666666">12.01000</span><span style="color: #008800; font-style: italic"> ; qtot -0.188</span>
<span style="color: #666666">38</span> hc <span style="color: #666666">1</span> lig H16 <span style="color: #666666">38</span> <span style="color: #666666">0.086700</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.101</span>
<span style="color: #666666">39</span> c3 <span style="color: #666666">1</span> lig C16 <span style="color: #666666">39</span> <span style="color: #666666">-0.091100</span> <span style="color: #666666">12.01000</span><span style="color: #008800; font-style: italic"> ; qtot -0.192</span>
<span style="color: #666666">40</span> hc <span style="color: #666666">1</span> lig H17 <span style="color: #666666">40</span> <span style="color: #666666">0.051367</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.141</span>
<span style="color: #666666">41</span> hc <span style="color: #666666">1</span> lig H18 <span style="color: #666666">41</span> <span style="color: #666666">0.051367</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.090</span>
<span style="color: #666666">42</span> hc <span style="color: #666666">1</span> lig H19 <span style="color: #666666">42</span> <span style="color: #666666">0.051367</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.038</span>
<span style="color: #666666">43</span> c <span style="color: #666666">1</span> lig C17 <span style="color: #666666">43</span> <span style="color: #666666">0.641101</span> <span style="color: #666666">12.01000</span><span style="color: #008800; font-style: italic"> ; qtot 0.603</span>
<span style="color: #666666">44</span> o <span style="color: #666666">1</span> lig O3 <span style="color: #666666">44</span> <span style="color: #666666">-0.552001</span> <span style="color: #666666">16.00000</span><span style="color: #008800; font-style: italic"> ; qtot 0.051</span>
<span style="color: #666666">45</span> oh <span style="color: #666666">1</span> lig O4 <span style="color: #666666">45</span> <span style="color: #666666">-0.606101</span> <span style="color: #666666">16.00000</span><span style="color: #008800; font-style: italic"> ; qtot -0.555</span>
<span style="color: #666666">46</span> ho <span style="color: #666666">1</span> lig H20 <span style="color: #666666">46</span> <span style="color: #666666">0.445000</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.110</span>
<span style="color: #666666">47</span> c3 <span style="color: #666666">1</span> lig C18 <span style="color: #666666">47</span> <span style="color: #666666">-0.041100</span> <span style="color: #666666">12.01000</span><span style="color: #008800; font-style: italic"> ; qtot -0.151</span>
<span style="color: #666666">48</span> c3 <span style="color: #666666">1</span> lig C19 <span style="color: #666666">48</span> <span style="color: #666666">-0.061700</span> <span style="color: #666666">12.01000</span><span style="color: #008800; font-style: italic"> ; qtot -0.213</span>
<span style="color: #666666">49</span> c3 <span style="color: #666666">1</span> lig C20 <span style="color: #666666">49</span> <span style="color: #666666">-0.092100</span> <span style="color: #666666">12.01000</span><span style="color: #008800; font-style: italic"> ; qtot -0.305</span>
<span style="color: #666666">50</span> hc <span style="color: #666666">1</span> lig H21 <span style="color: #666666">50</span> <span style="color: #666666">0.056700</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.249</span>
<span style="color: #666666">51</span> hc <span style="color: #666666">1</span> lig H22 <span style="color: #666666">51</span> <span style="color: #666666">0.039367</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.209</span>
<span style="color: #666666">52</span> hc <span style="color: #666666">1</span> lig H23 <span style="color: #666666">52</span> <span style="color: #666666">0.039367</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.170</span>
<span style="color: #666666">53</span> hc <span style="color: #666666">1</span> lig H24 <span style="color: #666666">53</span> <span style="color: #666666">0.039367</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.130</span>
<span style="color: #666666">54</span> c3 <span style="color: #666666">1</span> lig C21 <span style="color: #666666">54</span> <span style="color: #666666">-0.103400</span> <span style="color: #666666">12.01000</span><span style="color: #008800; font-style: italic"> ; qtot -0.234</span>
<span style="color: #666666">55</span> hc <span style="color: #666666">1</span> lig H25 <span style="color: #666666">55</span> <span style="color: #666666">0.075200</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.159</span>
<span style="color: #666666">56</span> hc <span style="color: #666666">1</span> lig H26 <span style="color: #666666">56</span> <span style="color: #666666">0.075200</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.083</span>
<span style="color: #666666">57</span> hc <span style="color: #666666">1</span> lig H27 <span style="color: #666666">57</span> <span style="color: #666666">0.052700</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.031</span>
<span style="color: #666666">58</span> hc <span style="color: #666666">1</span> lig H28 <span style="color: #666666">58</span> <span style="color: #666666">0.052700</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; XXX qtot 0.022</span>
<span style="color: #666666">59</span> n <span style="color: #666666">1</span> lig N2 <span style="color: #666666">59</span> <span style="color: #666666">-0.535901</span> <span style="color: #666666">14.01000</span><span style="color: #008800; font-style: italic"> ; qtot -0.514</span>
<span style="color: #666666">60</span> hn <span style="color: #666666">1</span> lig H29 <span style="color: #666666">60</span> <span style="color: #666666">0.355500</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.158</span>
<span style="color: #666666">61</span> c3 <span style="color: #666666">1</span> lig C22 <span style="color: #666666">61</span> <span style="color: #666666">0.038700</span> <span style="color: #666666">12.01000</span><span style="color: #008800; font-style: italic"> ; qtot -0.120</span>
<span style="color: #666666">62</span> h1 <span style="color: #666666">1</span> lig H30 <span style="color: #666666">62</span> <span style="color: #666666">0.087700</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.032</span>
<span style="color: #666666">63</span> c3 <span style="color: #666666">1</span> lig C23 <span style="color: #666666">63</span> <span style="color: #666666">0.137100</span> <span style="color: #666666">12.01000</span><span style="color: #008800; font-style: italic"> ; qtot 0.105</span>
<span style="color: #666666">64</span> h1 <span style="color: #666666">1</span> lig H31 <span style="color: #666666">64</span> <span style="color: #666666">0.068700</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot 0.174</span>
<span style="color: #666666">65</span> c3 <span style="color: #666666">1</span> lig C24 <span style="color: #666666">65</span> <span style="color: #666666">-0.133100</span> <span style="color: #666666">12.01000</span><span style="color: #008800; font-style: italic"> ; qtot 0.041</span>
<span style="color: #666666">66</span> hc <span style="color: #666666">1</span> lig H32 <span style="color: #666666">66</span> <span style="color: #666666">0.052367</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot 0.093</span>
<span style="color: #666666">67</span> hc <span style="color: #666666">1</span> lig H33 <span style="color: #666666">67</span> <span style="color: #666666">0.052367</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot 0.145</span>
<span style="color: #666666">68</span> hc <span style="color: #666666">1</span> lig H34 <span style="color: #666666">68</span> <span style="color: #666666">0.052367</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot 0.198</span>
<span style="color: #666666">69</span> oh <span style="color: #666666">1</span> lig O5 <span style="color: #666666">69</span> <span style="color: #666666">-0.609801</span> <span style="color: #666666">16.00000</span><span style="color: #008800; font-style: italic"> ; qtot -0.412</span>
<span style="color: #666666">70</span> ho <span style="color: #666666">1</span> lig H35 <span style="color: #666666">70</span> <span style="color: #666666">0.410000</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.002</span>
<span style="color: #666666">71</span> c <span style="color: #666666">1</span> lig C25 <span style="color: #666666">71</span> <span style="color: #666666">0.645101</span> <span style="color: #666666">12.01000</span><span style="color: #008800; font-style: italic"> ; qtot 0.643</span>
<span style="color: #666666">72</span> o <span style="color: #666666">1</span> lig O6 <span style="color: #666666">72</span> <span style="color: #666666">-0.623101</span> <span style="color: #666666">16.00000</span><span style="color: #008800; font-style: italic"> ; THR qtot 0.020</span>
<span style="color: #666666">73</span> n <span style="color: #666666">1</span> lig N3 <span style="color: #666666">73</span> <span style="color: #666666">-0.565901</span> <span style="color: #666666">14.01000</span><span style="color: #008800; font-style: italic"> ; qtot -0.546</span>
<span style="color: #666666">74</span> c3 <span style="color: #666666">1</span> lig C26 <span style="color: #666666">74</span> <span style="color: #666666">0.078300</span> <span style="color: #666666">12.01000</span><span style="color: #008800; font-style: italic"> ; qtot -0.468</span>
<span style="color: #666666">75</span> hn <span style="color: #666666">1</span> lig H36 <span style="color: #666666">75</span> <span style="color: #666666">0.340500</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.127</span>
<span style="color: #666666">76</span> h1 <span style="color: #666666">1</span> lig H37 <span style="color: #666666">76</span> <span style="color: #666666">0.042367</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.085</span>
<span style="color: #666666">77</span> h1 <span style="color: #666666">1</span> lig H38 <span style="color: #666666">77</span> <span style="color: #666666">0.042367</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.042</span>
<span style="color: #666666">78</span> h1 <span style="color: #666666">1</span> lig H39 <span style="color: #666666">78</span> <span style="color: #666666">0.042367</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; NME qtot -0.000</span></pre></div>可以看到, 前20个原子为ACE+19PRO, 最后20个原子为21THR+NME. 我们分别将这两组原子的总电荷加到与其相连的原子上. 具体而言, ACE+19PRO总电荷为0.043996, 将其加到N21上, 则N21电荷应为-0.551901+0.043996=-0.507905, 21THR+NME总电荷为-0.022001, 将其加到C25上, 则C25电荷应为0.640101-0.022001=0.6181. 我们可以看到, 这两组原子的总电荷都很接近零, 删除它们对20XXX电荷的影响比较小, 说明我们采用的方法比较合理.
修正电荷后, 我们再验证一下20XXX的总电荷是否为零. 由于数值计算的精度, 舍入, 截断等原因, 有时总电荷并不会恰好为零, 而是有微小的偏差. 对于我们的数据, 修正后20XXX的总电荷为-5e-5, 非常小, 但不是零. 所以, 我们再微调一下. 微调时可以任意选择一个原子的电荷, 给它增加等量的相反电荷, 也可以试着删除所有电荷的最后一位数字, 因为很多时候是最后一位数字导致的偏差. 至于具体选择哪个原子, 采用哪种方式, 没有定例, 怎么方便怎么来吧.
查看我们所得的数字, 删除最后一位数字并不方便, 删除N21电荷的最后一位数字5, 或将C25电荷最后增加05最方便. 这样调整后, 20XXX的总电荷为-1.5e-16, 足够接近零了.
<div class="highlight"><pre style="line-height:125%"><span></span>[ atoms ]<span style="color: #008800; font-style: italic"></span>
<span style="color: #008800; font-style: italic">; nr type resi res atom cgnr charge mass ; qtot bond_type</span>
<span style="color: #666666">1</span> c <span style="color: #666666">1</span> lig C <span style="color: #666666">1</span> <span style="color: #666666">0.654097</span> <span style="color: #666666">12.01000</span><span style="color: #008800; font-style: italic"> ; qtot 0.654</span>
<span style="color: #666666">2</span> o <span style="color: #666666">1</span> lig O <span style="color: #666666">2</span> <span style="color: #666666">-0.588101</span> <span style="color: #666666">16.00000</span><span style="color: #008800; font-style: italic"> ; qtot 0.066</span>
<span style="color: #666666">3</span> c3 <span style="color: #666666">1</span> lig C1 <span style="color: #666666">3</span> <span style="color: #666666">-0.175100</span> <span style="color: #666666">12.01000</span><span style="color: #008800; font-style: italic"> ; qtot -0.109</span>
<span style="color: #666666">4</span> hc <span style="color: #666666">1</span> lig H <span style="color: #666666">4</span> <span style="color: #666666">0.072700</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.036</span>
<span style="color: #666666">5</span> hc <span style="color: #666666">1</span> lig H1 <span style="color: #666666">5</span> <span style="color: #666666">0.072700</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot 0.036</span>
<span style="color: #666666">6</span> hc <span style="color: #666666">1</span> lig H2 <span style="color: #666666">6</span> <span style="color: #666666">0.072700</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; ACE qtot 0.109</span>
<span style="color: #666666">7</span> n <span style="color: #666666">1</span> lig N <span style="color: #666666">7</span> <span style="color: #666666">-0.475800</span> <span style="color: #666666">14.01000</span><span style="color: #008800; font-style: italic"> ; qtot -0.367</span>
<span style="color: #666666">8</span> c3 <span style="color: #666666">1</span> lig C2 <span style="color: #666666">8</span> <span style="color: #666666">0.078000</span> <span style="color: #666666">12.01000</span><span style="color: #008800; font-style: italic"> ; qtot -0.289</span>
<span style="color: #666666">9</span> h1 <span style="color: #666666">1</span> lig H3 <span style="color: #666666">9</span> <span style="color: #666666">0.062700</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.226</span>
<span style="color: #666666">10</span> h1 <span style="color: #666666">1</span> lig H4 <span style="color: #666666">10</span> <span style="color: #666666">0.062700</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.163</span>
<span style="color: #666666">11</span> c3 <span style="color: #666666">1</span> lig C3 <span style="color: #666666">11</span> <span style="color: #666666">-0.099400</span> <span style="color: #666666">12.01000</span><span style="color: #008800; font-style: italic"> ; qtot -0.263</span>
<span style="color: #666666">12</span> hc <span style="color: #666666">1</span> lig H5 <span style="color: #666666">12</span> <span style="color: #666666">0.058200</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.205</span>
<span style="color: #666666">13</span> hc <span style="color: #666666">1</span> lig H6 <span style="color: #666666">13</span> <span style="color: #666666">0.058200</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.146</span>
<span style="color: #666666">14</span> c3 <span style="color: #666666">1</span> lig C4 <span style="color: #666666">14</span> <span style="color: #666666">-0.090400</span> <span style="color: #666666">12.01000</span><span style="color: #008800; font-style: italic"> ; qtot -0.237</span>
<span style="color: #666666">15</span> hc <span style="color: #666666">1</span> lig H7 <span style="color: #666666">15</span> <span style="color: #666666">0.067200</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.170</span>
<span style="color: #666666">16</span> hc <span style="color: #666666">1</span> lig H8 <span style="color: #666666">16</span> <span style="color: #666666">0.067200</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.102</span>
<span style="color: #666666">17</span> c3 <span style="color: #666666">1</span> lig C5 <span style="color: #666666">17</span> <span style="color: #666666">0.025700</span> <span style="color: #666666">12.01000</span><span style="color: #008800; font-style: italic"> ; qtot -0.077</span>
<span style="color: #666666">18</span> h1 <span style="color: #666666">1</span> lig H9 <span style="color: #666666">18</span> <span style="color: #666666">0.088700</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot 0.012</span>
<span style="color: #666666">19</span> c <span style="color: #666666">1</span> lig C6 <span style="color: #666666">19</span> <span style="color: #666666">0.656101</span> <span style="color: #666666">12.01000</span><span style="color: #008800; font-style: italic"> ; qtot 0.668</span>
<span style="color: #666666">20</span> o <span style="color: #666666">1</span> lig O1 <span style="color: #666666">20</span> <span style="color: #666666">-0.624101</span> <span style="color: #666666">16.00000</span><span style="color: #008800; font-style: italic"> ; PRO qtot 0.044</span>
<span style="color: #666666">21</span> n <span style="color: #666666">1</span> lig N1 <span style="color: #666666">21</span> <span style="color: #666666">-0.50790</span> <span style="color: #666666">14.01000</span><span style="color: #008800; font-style: italic"> ; 删除末位的5</span>
<span style="color: #666666">22</span> hn <span style="color: #666666">1</span> lig H10 <span style="color: #666666">22</span> <span style="color: #666666">0.328500</span> <span style="color: #666666">1.00800</span>
<span style="color: #666666">23</span> c3 <span style="color: #666666">1</span> lig C7 <span style="color: #666666">23</span> <span style="color: #666666">0.050700</span> <span style="color: #666666">12.01000</span>
<span style="color: #666666">24</span> h1 <span style="color: #666666">1</span> lig H11 <span style="color: #666666">24</span> <span style="color: #666666">0.088700</span> <span style="color: #666666">1.00800</span>
<span style="color: #666666">25</span> c <span style="color: #666666">1</span> lig C8 <span style="color: #666666">25</span> <span style="color: #666666">0.6181</span> <span style="color: #666666">12.01000</span>
<span style="color: #666666">26</span> o <span style="color: #666666">1</span> lig O2 <span style="color: #666666">26</span> <span style="color: #666666">-0.639101</span> <span style="color: #666666">16.00000</span>
<span style="color: #666666">27</span> ca <span style="color: #666666">1</span> lig C9 <span style="color: #666666">27</span> <span style="color: #666666">-0.129000</span> <span style="color: #666666">12.01000</span>
<span style="color: #666666">28</span> ca <span style="color: #666666">1</span> lig C10 <span style="color: #666666">28</span> <span style="color: #666666">-0.112000</span> <span style="color: #666666">12.01000</span>
<span style="color: #666666">29</span> ca <span style="color: #666666">1</span> lig C11 <span style="color: #666666">29</span> <span style="color: #666666">-0.095300</span> <span style="color: #666666">12.01000</span>
<span style="color: #666666">30</span> ca <span style="color: #666666">1</span> lig C12 <span style="color: #666666">30</span> <span style="color: #666666">-0.112000</span> <span style="color: #666666">12.01000</span>
<span style="color: #666666">31</span> ca <span style="color: #666666">1</span> lig C13 <span style="color: #666666">31</span> <span style="color: #666666">-0.129000</span> <span style="color: #666666">12.01000</span>
<span style="color: #666666">32</span> ca <span style="color: #666666">1</span> lig C14 <span style="color: #666666">32</span> <span style="color: #666666">-0.069300</span> <span style="color: #666666">12.01000</span>
<span style="color: #666666">33</span> ha <span style="color: #666666">1</span> lig H12 <span style="color: #666666">33</span> <span style="color: #666666">0.133000</span> <span style="color: #666666">1.00800</span>
<span style="color: #666666">34</span> ha <span style="color: #666666">1</span> lig H13 <span style="color: #666666">34</span> <span style="color: #666666">0.144000</span> <span style="color: #666666">1.00800</span>
<span style="color: #666666">35</span> ha <span style="color: #666666">1</span> lig H14 <span style="color: #666666">35</span> <span style="color: #666666">0.144000</span> <span style="color: #666666">1.00800</span>
<span style="color: #666666">36</span> ha <span style="color: #666666">1</span> lig H15 <span style="color: #666666">36</span> <span style="color: #666666">0.133000</span> <span style="color: #666666">1.00800</span>
<span style="color: #666666">37</span> c3 <span style="color: #666666">1</span> lig C15 <span style="color: #666666">37</span> <span style="color: #666666">-0.056400</span> <span style="color: #666666">12.01000</span>
<span style="color: #666666">38</span> hc <span style="color: #666666">1</span> lig H16 <span style="color: #666666">38</span> <span style="color: #666666">0.086700</span> <span style="color: #666666">1.00800</span>
<span style="color: #666666">39</span> c3 <span style="color: #666666">1</span> lig C16 <span style="color: #666666">39</span> <span style="color: #666666">-0.091100</span> <span style="color: #666666">12.01000</span>
<span style="color: #666666">40</span> hc <span style="color: #666666">1</span> lig H17 <span style="color: #666666">40</span> <span style="color: #666666">0.051367</span> <span style="color: #666666">1.00800</span>
<span style="color: #666666">41</span> hc <span style="color: #666666">1</span> lig H18 <span style="color: #666666">41</span> <span style="color: #666666">0.051367</span> <span style="color: #666666">1.00800</span>
<span style="color: #666666">42</span> hc <span style="color: #666666">1</span> lig H19 <span style="color: #666666">42</span> <span style="color: #666666">0.051367</span> <span style="color: #666666">1.00800</span>
<span style="color: #666666">43</span> c <span style="color: #666666">1</span> lig C17 <span style="color: #666666">43</span> <span style="color: #666666">0.641101</span> <span style="color: #666666">12.01000</span>
<span style="color: #666666">44</span> o <span style="color: #666666">1</span> lig O3 <span style="color: #666666">44</span> <span style="color: #666666">-0.552001</span> <span style="color: #666666">16.00000</span>
<span style="color: #666666">45</span> oh <span style="color: #666666">1</span> lig O4 <span style="color: #666666">45</span> <span style="color: #666666">-0.606101</span> <span style="color: #666666">16.00000</span>
<span style="color: #666666">46</span> ho <span style="color: #666666">1</span> lig H20 <span style="color: #666666">46</span> <span style="color: #666666">0.445000</span> <span style="color: #666666">1.00800</span>
<span style="color: #666666">47</span> c3 <span style="color: #666666">1</span> lig C18 <span style="color: #666666">47</span> <span style="color: #666666">-0.041100</span> <span style="color: #666666">12.01000</span>
<span style="color: #666666">48</span> c3 <span style="color: #666666">1</span> lig C19 <span style="color: #666666">48</span> <span style="color: #666666">-0.061700</span> <span style="color: #666666">12.01000</span>
<span style="color: #666666">49</span> c3 <span style="color: #666666">1</span> lig C20 <span style="color: #666666">49</span> <span style="color: #666666">-0.092100</span> <span style="color: #666666">12.01000</span>
<span style="color: #666666">50</span> hc <span style="color: #666666">1</span> lig H21 <span style="color: #666666">50</span> <span style="color: #666666">0.056700</span> <span style="color: #666666">1.00800</span>
<span style="color: #666666">51</span> hc <span style="color: #666666">1</span> lig H22 <span style="color: #666666">51</span> <span style="color: #666666">0.039367</span> <span style="color: #666666">1.00800</span>
<span style="color: #666666">52</span> hc <span style="color: #666666">1</span> lig H23 <span style="color: #666666">52</span> <span style="color: #666666">0.039367</span> <span style="color: #666666">1.00800</span>
<span style="color: #666666">53</span> hc <span style="color: #666666">1</span> lig H24 <span style="color: #666666">53</span> <span style="color: #666666">0.039367</span> <span style="color: #666666">1.00800</span>
<span style="color: #666666">54</span> c3 <span style="color: #666666">1</span> lig C21 <span style="color: #666666">54</span> <span style="color: #666666">-0.103400</span> <span style="color: #666666">12.01000</span>
<span style="color: #666666">55</span> hc <span style="color: #666666">1</span> lig H25 <span style="color: #666666">55</span> <span style="color: #666666">0.075200</span> <span style="color: #666666">1.00800</span>
<span style="color: #666666">56</span> hc <span style="color: #666666">1</span> lig H26 <span style="color: #666666">56</span> <span style="color: #666666">0.075200</span> <span style="color: #666666">1.00800</span>
<span style="color: #666666">57</span> hc <span style="color: #666666">1</span> lig H27 <span style="color: #666666">57</span> <span style="color: #666666">0.052700</span> <span style="color: #666666">1.00800</span>
<span style="color: #666666">58</span> hc <span style="color: #666666">1</span> lig H28 <span style="color: #666666">58</span> <span style="color: #666666">0.052700</span> <span style="color: #666666">1.00800</span>
<span style="color: #666666">59</span> n <span style="color: #666666">1</span> lig N2 <span style="color: #666666">59</span> <span style="color: #666666">-0.535901</span> <span style="color: #666666">14.01000</span><span style="color: #008800; font-style: italic"> ; qtot -0.514</span>
<span style="color: #666666">60</span> hn <span style="color: #666666">1</span> lig H29 <span style="color: #666666">60</span> <span style="color: #666666">0.355500</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.158</span>
<span style="color: #666666">61</span> c3 <span style="color: #666666">1</span> lig C22 <span style="color: #666666">61</span> <span style="color: #666666">0.038700</span> <span style="color: #666666">12.01000</span><span style="color: #008800; font-style: italic"> ; qtot -0.120</span>
<span style="color: #666666">62</span> h1 <span style="color: #666666">1</span> lig H30 <span style="color: #666666">62</span> <span style="color: #666666">0.087700</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.032</span>
<span style="color: #666666">63</span> c3 <span style="color: #666666">1</span> lig C23 <span style="color: #666666">63</span> <span style="color: #666666">0.137100</span> <span style="color: #666666">12.01000</span><span style="color: #008800; font-style: italic"> ; qtot 0.105</span>
<span style="color: #666666">64</span> h1 <span style="color: #666666">1</span> lig H31 <span style="color: #666666">64</span> <span style="color: #666666">0.068700</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot 0.174</span>
<span style="color: #666666">65</span> c3 <span style="color: #666666">1</span> lig C24 <span style="color: #666666">65</span> <span style="color: #666666">-0.133100</span> <span style="color: #666666">12.01000</span><span style="color: #008800; font-style: italic"> ; qtot 0.041</span>
<span style="color: #666666">66</span> hc <span style="color: #666666">1</span> lig H32 <span style="color: #666666">66</span> <span style="color: #666666">0.052367</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot 0.093</span>
<span style="color: #666666">67</span> hc <span style="color: #666666">1</span> lig H33 <span style="color: #666666">67</span> <span style="color: #666666">0.052367</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot 0.145</span>
<span style="color: #666666">68</span> hc <span style="color: #666666">1</span> lig H34 <span style="color: #666666">68</span> <span style="color: #666666">0.052367</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot 0.198</span>
<span style="color: #666666">69</span> oh <span style="color: #666666">1</span> lig O5 <span style="color: #666666">69</span> <span style="color: #666666">-0.609801</span> <span style="color: #666666">16.00000</span><span style="color: #008800; font-style: italic"> ; qtot -0.412</span>
<span style="color: #666666">70</span> ho <span style="color: #666666">1</span> lig H35 <span style="color: #666666">70</span> <span style="color: #666666">0.410000</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.002</span>
<span style="color: #666666">71</span> c <span style="color: #666666">1</span> lig C25 <span style="color: #666666">71</span> <span style="color: #666666">0.645101</span> <span style="color: #666666">12.01000</span><span style="color: #008800; font-style: italic"> ; qtot 0.643</span>
<span style="color: #666666">72</span> o <span style="color: #666666">1</span> lig O6 <span style="color: #666666">72</span> <span style="color: #666666">-0.623101</span> <span style="color: #666666">16.00000</span><span style="color: #008800; font-style: italic"> ; THR qtot 0.020</span>
<span style="color: #666666">73</span> n <span style="color: #666666">1</span> lig N3 <span style="color: #666666">73</span> <span style="color: #666666">-0.565901</span> <span style="color: #666666">14.01000</span><span style="color: #008800; font-style: italic"> ; qtot -0.546</span>
<span style="color: #666666">74</span> c3 <span style="color: #666666">1</span> lig C26 <span style="color: #666666">74</span> <span style="color: #666666">0.078300</span> <span style="color: #666666">12.01000</span><span style="color: #008800; font-style: italic"> ; qtot -0.468</span>
<span style="color: #666666">75</span> hn <span style="color: #666666">1</span> lig H36 <span style="color: #666666">75</span> <span style="color: #666666">0.340500</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.127</span>
<span style="color: #666666">76</span> h1 <span style="color: #666666">1</span> lig H37 <span style="color: #666666">76</span> <span style="color: #666666">0.042367</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.085</span>
<span style="color: #666666">77</span> h1 <span style="color: #666666">1</span> lig H38 <span style="color: #666666">77</span> <span style="color: #666666">0.042367</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.042</span>
<span style="color: #666666">78</span> h1 <span style="color: #666666">1</span> lig H39 <span style="color: #666666">78</span> <span style="color: #666666">0.042367</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; NME qtot -0.000</span></pre></div>6. 调整编号, 使其与蛋白拓扑中的一致: 2-1_调整top原子编号.js
20XXX最终是要合并到蛋白拓扑中的, 而且我们前面已经在蛋白拓扑中为它预留了位置, 所以其原子编号必须与最终蛋白拓扑中的一致. 此外, 也需要将前后相连残基19PRO, 21THR的原子编号调整至与蛋白拓扑中的一致, 方便后面添加成键项.
回顾前面的数字, 蛋白拓扑中19PRO的原子编号从273开始, 而LIG中的则从7开始, 所以我们再次使用脚本2-1_调整top原子编号.js, 设定7:999:273, 这样就得到了调整编号后的LIG拓扑.
<div class="highlight"><pre style="line-height:125%"><span></span>[ atoms ]<span style="color: #008800; font-style: italic"></span>
<span style="color: #008800; font-style: italic">; nr type resi res atom cgnr charge mass ; qtot bond_type</span>
<span style="color: #666666">1</span> c <span style="color: #666666">1</span> lig C <span style="color: #666666">1</span> <span style="color: #666666">0.654097</span> <span style="color: #666666">12.01000</span><span style="color: #008800; font-style: italic"> ; qtot 0.654</span>
<span style="color: #666666">2</span> o <span style="color: #666666">1</span> lig O <span style="color: #666666">2</span> <span style="color: #666666">-0.588101</span> <span style="color: #666666">16.00000</span><span style="color: #008800; font-style: italic"> ; qtot 0.066</span>
<span style="color: #666666">3</span> c3 <span style="color: #666666">1</span> lig C1 <span style="color: #666666">3</span> <span style="color: #666666">-0.175100</span> <span style="color: #666666">12.01000</span><span style="color: #008800; font-style: italic"> ; qtot -0.109</span>
<span style="color: #666666">4</span> hc <span style="color: #666666">1</span> lig H <span style="color: #666666">4</span> <span style="color: #666666">0.072700</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.036</span>
<span style="color: #666666">5</span> hc <span style="color: #666666">1</span> lig H1 <span style="color: #666666">5</span> <span style="color: #666666">0.072700</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot 0.036</span>
<span style="color: #666666">6</span> hc <span style="color: #666666">1</span> lig H2 <span style="color: #666666">6</span> <span style="color: #666666">0.072700</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; ACE qtot 0.109</span>
<span style="color: #666666">273</span> n <span style="color: #666666">1</span> lig N <span style="color: #666666">7</span> <span style="color: #666666">-0.475800</span> <span style="color: #666666">14.01000</span><span style="color: #008800; font-style: italic"> ; qtot -0.367</span>
<span style="color: #666666">274</span> c3 <span style="color: #666666">1</span> lig C2 <span style="color: #666666">8</span> <span style="color: #666666">0.078000</span> <span style="color: #666666">12.01000</span><span style="color: #008800; font-style: italic"> ; qtot -0.289</span>
<span style="color: #666666">275</span> h1 <span style="color: #666666">1</span> lig H3 <span style="color: #666666">9</span> <span style="color: #666666">0.062700</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.226</span>
<span style="color: #666666">276</span> h1 <span style="color: #666666">1</span> lig H4 <span style="color: #666666">10</span> <span style="color: #666666">0.062700</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.163</span>
<span style="color: #666666">277</span> c3 <span style="color: #666666">1</span> lig C3 <span style="color: #666666">11</span> <span style="color: #666666">-0.099400</span> <span style="color: #666666">12.01000</span><span style="color: #008800; font-style: italic"> ; qtot -0.263</span>
<span style="color: #666666">278</span> hc <span style="color: #666666">1</span> lig H5 <span style="color: #666666">12</span> <span style="color: #666666">0.058200</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.205</span>
<span style="color: #666666">279</span> hc <span style="color: #666666">1</span> lig H6 <span style="color: #666666">13</span> <span style="color: #666666">0.058200</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.146</span>
<span style="color: #666666">280</span> c3 <span style="color: #666666">1</span> lig C4 <span style="color: #666666">14</span> <span style="color: #666666">-0.090400</span> <span style="color: #666666">12.01000</span><span style="color: #008800; font-style: italic"> ; qtot -0.237</span>
<span style="color: #666666">281</span> hc <span style="color: #666666">1</span> lig H7 <span style="color: #666666">15</span> <span style="color: #666666">0.067200</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.170</span>
<span style="color: #666666">282</span> hc <span style="color: #666666">1</span> lig H8 <span style="color: #666666">16</span> <span style="color: #666666">0.067200</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.102</span>
<span style="color: #666666">283</span> c3 <span style="color: #666666">1</span> lig C5 <span style="color: #666666">17</span> <span style="color: #666666">0.025700</span> <span style="color: #666666">12.01000</span><span style="color: #008800; font-style: italic"> ; qtot -0.077</span>
<span style="color: #666666">284</span> h1 <span style="color: #666666">1</span> lig H9 <span style="color: #666666">18</span> <span style="color: #666666">0.088700</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot 0.012</span>
<span style="color: #666666">285</span> c <span style="color: #666666">1</span> lig C6 <span style="color: #666666">19</span> <span style="color: #666666">0.656101</span> <span style="color: #666666">12.01000</span><span style="color: #008800; font-style: italic"> ; qtot 0.668</span>
<span style="color: #666666">286</span> o <span style="color: #666666">1</span> lig O1 <span style="color: #666666">20</span> <span style="color: #666666">-0.624101</span> <span style="color: #666666">16.00000</span><span style="color: #008800; font-style: italic"> ; PRO qtot 0.044</span>
<span style="color: #666666">287</span> n <span style="color: #666666">1</span> lig N1 <span style="color: #666666">21</span> <span style="color: #666666">-0.50790</span> <span style="color: #666666">14.01000</span>
<span style="color: #666666">288</span> hn <span style="color: #666666">1</span> lig H10 <span style="color: #666666">22</span> <span style="color: #666666">0.328500</span> <span style="color: #666666">1.00800</span>
<span style="color: #666666">289</span> c3 <span style="color: #666666">1</span> lig C7 <span style="color: #666666">23</span> <span style="color: #666666">0.050700</span> <span style="color: #666666">12.01000</span>
<span style="color: #666666">290</span> h1 <span style="color: #666666">1</span> lig H11 <span style="color: #666666">24</span> <span style="color: #666666">0.088700</span> <span style="color: #666666">1.00800</span>
<span style="color: #666666">291</span> c <span style="color: #666666">1</span> lig C8 <span style="color: #666666">25</span> <span style="color: #666666">0.6181</span> <span style="color: #666666">12.01000</span>
<span style="color: #666666">292</span> o <span style="color: #666666">1</span> lig O2 <span style="color: #666666">26</span> <span style="color: #666666">-0.639101</span> <span style="color: #666666">16.00000</span>
<span style="color: #666666">293</span> ca <span style="color: #666666">1</span> lig C9 <span style="color: #666666">27</span> <span style="color: #666666">-0.129000</span> <span style="color: #666666">12.01000</span>
<span style="color: #666666">294</span> ca <span style="color: #666666">1</span> lig C10 <span style="color: #666666">28</span> <span style="color: #666666">-0.112000</span> <span style="color: #666666">12.01000</span>
<span style="color: #666666">295</span> ca <span style="color: #666666">1</span> lig C11 <span style="color: #666666">29</span> <span style="color: #666666">-0.095300</span> <span style="color: #666666">12.01000</span>
<span style="color: #666666">296</span> ca <span style="color: #666666">1</span> lig C12 <span style="color: #666666">30</span> <span style="color: #666666">-0.112000</span> <span style="color: #666666">12.01000</span>
<span style="color: #666666">297</span> ca <span style="color: #666666">1</span> lig C13 <span style="color: #666666">31</span> <span style="color: #666666">-0.129000</span> <span style="color: #666666">12.01000</span>
<span style="color: #666666">298</span> ca <span style="color: #666666">1</span> lig C14 <span style="color: #666666">32</span> <span style="color: #666666">-0.069300</span> <span style="color: #666666">12.01000</span>
<span style="color: #666666">299</span> ha <span style="color: #666666">1</span> lig H12 <span style="color: #666666">33</span> <span style="color: #666666">0.133000</span> <span style="color: #666666">1.00800</span>
<span style="color: #666666">300</span> ha <span style="color: #666666">1</span> lig H13 <span style="color: #666666">34</span> <span style="color: #666666">0.144000</span> <span style="color: #666666">1.00800</span>
<span style="color: #666666">301</span> ha <span style="color: #666666">1</span> lig H14 <span style="color: #666666">35</span> <span style="color: #666666">0.144000</span> <span style="color: #666666">1.00800</span>
<span style="color: #666666">302</span> ha <span style="color: #666666">1</span> lig H15 <span style="color: #666666">36</span> <span style="color: #666666">0.133000</span> <span style="color: #666666">1.00800</span>
<span style="color: #666666">303</span> c3 <span style="color: #666666">1</span> lig C15 <span style="color: #666666">37</span> <span style="color: #666666">-0.056400</span> <span style="color: #666666">12.01000</span>
<span style="color: #666666">304</span> hc <span style="color: #666666">1</span> lig H16 <span style="color: #666666">38</span> <span style="color: #666666">0.086700</span> <span style="color: #666666">1.00800</span>
<span style="color: #666666">305</span> c3 <span style="color: #666666">1</span> lig C16 <span style="color: #666666">39</span> <span style="color: #666666">-0.091100</span> <span style="color: #666666">12.01000</span>
<span style="color: #666666">306</span> hc <span style="color: #666666">1</span> lig H17 <span style="color: #666666">40</span> <span style="color: #666666">0.051367</span> <span style="color: #666666">1.00800</span>
<span style="color: #666666">307</span> hc <span style="color: #666666">1</span> lig H18 <span style="color: #666666">41</span> <span style="color: #666666">0.051367</span> <span style="color: #666666">1.00800</span>
<span style="color: #666666">308</span> hc <span style="color: #666666">1</span> lig H19 <span style="color: #666666">42</span> <span style="color: #666666">0.051367</span> <span style="color: #666666">1.00800</span>
<span style="color: #666666">309</span> c <span style="color: #666666">1</span> lig C17 <span style="color: #666666">43</span> <span style="color: #666666">0.641101</span> <span style="color: #666666">12.01000</span>
<span style="color: #666666">310</span> o <span style="color: #666666">1</span> lig O3 <span style="color: #666666">44</span> <span style="color: #666666">-0.552001</span> <span style="color: #666666">16.00000</span>
<span style="color: #666666">311</span> oh <span style="color: #666666">1</span> lig O4 <span style="color: #666666">45</span> <span style="color: #666666">-0.606101</span> <span style="color: #666666">16.00000</span>
<span style="color: #666666">312</span> ho <span style="color: #666666">1</span> lig H20 <span style="color: #666666">46</span> <span style="color: #666666">0.445000</span> <span style="color: #666666">1.00800</span>
<span style="color: #666666">313</span> c3 <span style="color: #666666">1</span> lig C18 <span style="color: #666666">47</span> <span style="color: #666666">-0.041100</span> <span style="color: #666666">12.01000</span>
<span style="color: #666666">314</span> c3 <span style="color: #666666">1</span> lig C19 <span style="color: #666666">48</span> <span style="color: #666666">-0.061700</span> <span style="color: #666666">12.01000</span>
<span style="color: #666666">315</span> c3 <span style="color: #666666">1</span> lig C20 <span style="color: #666666">49</span> <span style="color: #666666">-0.092100</span> <span style="color: #666666">12.01000</span>
<span style="color: #666666">316</span> hc <span style="color: #666666">1</span> lig H21 <span style="color: #666666">50</span> <span style="color: #666666">0.056700</span> <span style="color: #666666">1.00800</span>
<span style="color: #666666">317</span> hc <span style="color: #666666">1</span> lig H22 <span style="color: #666666">51</span> <span style="color: #666666">0.039367</span> <span style="color: #666666">1.00800</span>
<span style="color: #666666">318</span> hc <span style="color: #666666">1</span> lig H23 <span style="color: #666666">52</span> <span style="color: #666666">0.039367</span> <span style="color: #666666">1.00800</span>
<span style="color: #666666">319</span> hc <span style="color: #666666">1</span> lig H24 <span style="color: #666666">53</span> <span style="color: #666666">0.039367</span> <span style="color: #666666">1.00800</span>
<span style="color: #666666">320</span> c3 <span style="color: #666666">1</span> lig C21 <span style="color: #666666">54</span> <span style="color: #666666">-0.103400</span> <span style="color: #666666">12.01000</span>
<span style="color: #666666">321</span> hc <span style="color: #666666">1</span> lig H25 <span style="color: #666666">55</span> <span style="color: #666666">0.075200</span> <span style="color: #666666">1.00800</span>
<span style="color: #666666">322</span> hc <span style="color: #666666">1</span> lig H26 <span style="color: #666666">56</span> <span style="color: #666666">0.075200</span> <span style="color: #666666">1.00800</span>
<span style="color: #666666">323</span> hc <span style="color: #666666">1</span> lig H27 <span style="color: #666666">57</span> <span style="color: #666666">0.052700</span> <span style="color: #666666">1.00800</span>
<span style="color: #666666">324</span> hc <span style="color: #666666">1</span> lig H28 <span style="color: #666666">58</span> <span style="color: #666666">0.052700</span> <span style="color: #666666">1.00800</span>
<span style="color: #666666">325</span> n <span style="color: #666666">1</span> lig N2 <span style="color: #666666">59</span> <span style="color: #666666">-0.535901</span> <span style="color: #666666">14.01000</span><span style="color: #008800; font-style: italic"> ; qtot -0.514</span>
<span style="color: #666666">326</span> hn <span style="color: #666666">1</span> lig H29 <span style="color: #666666">60</span> <span style="color: #666666">0.355500</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.158</span>
<span style="color: #666666">327</span> c3 <span style="color: #666666">1</span> lig C22 <span style="color: #666666">61</span> <span style="color: #666666">0.038700</span> <span style="color: #666666">12.01000</span><span style="color: #008800; font-style: italic"> ; qtot -0.120</span>
<span style="color: #666666">328</span> h1 <span style="color: #666666">1</span> lig H30 <span style="color: #666666">62</span> <span style="color: #666666">0.087700</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.032</span>
<span style="color: #666666">329</span> c3 <span style="color: #666666">1</span> lig C23 <span style="color: #666666">63</span> <span style="color: #666666">0.137100</span> <span style="color: #666666">12.01000</span><span style="color: #008800; font-style: italic"> ; qtot 0.105</span>
<span style="color: #666666">330</span> h1 <span style="color: #666666">1</span> lig H31 <span style="color: #666666">64</span> <span style="color: #666666">0.068700</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot 0.174</span>
<span style="color: #666666">331</span> c3 <span style="color: #666666">1</span> lig C24 <span style="color: #666666">65</span> <span style="color: #666666">-0.133100</span> <span style="color: #666666">12.01000</span><span style="color: #008800; font-style: italic"> ; qtot 0.041</span>
<span style="color: #666666">332</span> hc <span style="color: #666666">1</span> lig H32 <span style="color: #666666">66</span> <span style="color: #666666">0.052367</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot 0.093</span>
<span style="color: #666666">333</span> hc <span style="color: #666666">1</span> lig H33 <span style="color: #666666">67</span> <span style="color: #666666">0.052367</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot 0.145</span>
<span style="color: #666666">334</span> hc <span style="color: #666666">1</span> lig H34 <span style="color: #666666">68</span> <span style="color: #666666">0.052367</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot 0.198</span>
<span style="color: #666666">335</span> oh <span style="color: #666666">1</span> lig O5 <span style="color: #666666">69</span> <span style="color: #666666">-0.609801</span> <span style="color: #666666">16.00000</span><span style="color: #008800; font-style: italic"> ; qtot -0.412</span>
<span style="color: #666666">336</span> ho <span style="color: #666666">1</span> lig H35 <span style="color: #666666">70</span> <span style="color: #666666">0.410000</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.002</span>
<span style="color: #666666">337</span> c <span style="color: #666666">1</span> lig C25 <span style="color: #666666">71</span> <span style="color: #666666">0.645101</span> <span style="color: #666666">12.01000</span><span style="color: #008800; font-style: italic"> ; qtot 0.643</span>
<span style="color: #666666">338</span> o <span style="color: #666666">1</span> lig O6 <span style="color: #666666">72</span> <span style="color: #666666">-0.623101</span> <span style="color: #666666">16.00000</span><span style="color: #008800; font-style: italic"> ; THR qtot 0.020</span>
<span style="color: #666666">339</span> n <span style="color: #666666">1</span> lig N3 <span style="color: #666666">73</span> <span style="color: #666666">-0.565901</span> <span style="color: #666666">14.01000</span><span style="color: #008800; font-style: italic"> ; qtot -0.546</span>
<span style="color: #666666">340</span> c3 <span style="color: #666666">1</span> lig C26 <span style="color: #666666">74</span> <span style="color: #666666">0.078300</span> <span style="color: #666666">12.01000</span><span style="color: #008800; font-style: italic"> ; qtot -0.468</span>
<span style="color: #666666">341</span> hn <span style="color: #666666">1</span> lig H36 <span style="color: #666666">75</span> <span style="color: #666666">0.340500</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.127</span>
<span style="color: #666666">342</span> h1 <span style="color: #666666">1</span> lig H37 <span style="color: #666666">76</span> <span style="color: #666666">0.042367</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.085</span>
<span style="color: #666666">343</span> h1 <span style="color: #666666">1</span> lig H38 <span style="color: #666666">77</span> <span style="color: #666666">0.042367</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; qtot -0.042</span>
<span style="color: #666666">344</span> h1 <span style="color: #666666">1</span> lig H39 <span style="color: #666666">78</span> <span style="color: #666666">0.042367</span> <span style="color: #666666">1.00800</span><span style="color: #008800; font-style: italic"> ; NME qtot -0.000</span></pre></div>7. 抽取非标准残基的原子及其参与的成键项: 2-3_保留top原子.js
将20XXX合并到蛋白拓扑中时, 需要其自身原子, 自身原子间的成键项, 自身原子与19PRO, 21THR的成键项, 由于这些成键项在LIG的拓扑中都是存在的, 所以我们可以直接抽取出来使用. 这也是我们前面创建LIG拓扑时使用19PRO, 21THR的原因.
使用步骤6中调整好编号的拓扑, 启动脚本2-3_保留top原子.js, 保留287:324
这样就得到了所需的原子及其成键项.
注意: 这一步骤在先前的教程中是通过两步完成的: 先添加需要的成键项获得20XXX与前后残基的成键项, 再删除不属于20XXX的原子获得其自身原子及其成键项. 这种方法可行, 但稍麻烦些.
8. 合并所有非标准残基拓扑到蛋白拓扑
将步骤7所得拓扑[ atoms ]部分复制粘贴到蛋白拓扑的对应位置, 完成最终蛋白拓扑的[ atoms ]部分.
将步骤7所得的成键项, 复制粘贴到蛋白拓扑的相应位置, 完成最终蛋白拓扑的成键部分.
9. 测试所得拓扑
使用得到的拓扑进行短时间的模拟, 确认不存在问题.
由于蛋白中添加了非标准残基, 所以进行位置限制动力学时, 非标准残基原子也要限制. 此外, 设置温度耦合组时要注意将非标准残基包含在蛋白组中.
几点说明
此方法看似步骤很多, 是因为我写得详细, 实际操作并不复杂, 难度低于创建rtp的方法. 主要难点在于数数, 数对原子编号.
此方法比生成rtp的方法更通用, 几乎可以将任何分子连接到蛋白上.
将非标准残基拓扑与蛋白拓扑进行组合时, 可以简单地将非标准残基追加到最后, 但这样做残基编号, 尤其是与非标准残基前后相连的残基编号与GAFF拓扑中的区别较大, 后面获得成键项时会不方便, 所以还是尽量放在原来的对应位置吧.
删除非标准残基的蛋白拓扑, 删除封端基团的GAFF拓扑, 对原子编号进行调整, 保证连续后都可以进行简单的模拟, 以验证拓扑是否存在问题.
你可以下载添加了布洛芬的1crn, 自己试着处理
你还可以下载另一个我瞎改后的1crn, 里面使用长的碳链将两个距离很远的残基连起来了. 这种情况也可以处理, 虽然稍微麻烦点.
就这些吧. 完了.