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layout: post title: Amber构建脂分子的方法 categories:

【按】以下翻译自Amber 16手册.

13.6.2 使用GLYCAM-06参数构建脂分子

遵循这里讲述的步骤, 用户可以得到一个简单的脂分子, 但在构建过程中我们没有考虑它的轴向排列情况. 脂双层通常放置在直角坐标系统的(x, y)平面内, 这要求每个脂分子以从亲水"头"端到憎水"尾"端的顺序沿z方向排列. 通过载入已经沿z轴正确排列好的模板PDB文件, 这容易完成.

本例中我们使用的脂分子是二肉豆蔻酰磷脂酰胆碱(1,2-dimyristoyl-sn-glycero-3-phosphocholine), 或简称DMPC, 它由四个片段组成: 胆碱头基CHO, 磷酯头基PGL, sn-1链肉豆蔻酸尾基MYR, sn-2链肉豆蔻酸尾基MY2. 分子结构与原子编号如图13.3(为清晰起见, 未显示氢原子和原子电荷), 其中残基间的成键点以虚线表示. 本教程将只使用每个片段prep文件. 这些prep文件开始是pdb格式, 然后使用antechamber将其重新格式化为prep文件, 并添加了与GLYCAM兼容的电荷. prep文件数据库(GLYCAM_lipids_06h.prep)中已经包含了四个残基的相关文件.

13.6.2.1 示例: 使用LEaP构建脂分子

为了使用GLYCAM-06参数集构建一个脂分子, 你不需要加载整个GLYCAM pre文件, 但当使用默认的leaprc.GLYCAM_06j-1时它会自动载入. 注意, 使用下面的命令构建的脂分子还没有沿需要的方向对齐, 可能无法马上用于创建脂双层. 具体命令如下

<div class="highlight" style="background: #f8f8f8"><pre style="line-height: 125%"><span></span><span style="color: #AA22FF">source</span><span style="color: #bbbbbb"> </span>leaprc.GLYCAM_06j-1<span style="color: #bbbbbb"> </span><span style="color: #008800; font-style: italic">#</span><span style="color: #bbbbbb"> </span><span style="color: #008800; font-style: italic">source</span><span style="color: #bbbbbb"> </span><span style="color: #008800; font-style: italic">GLYCAM-06的</span><span style="color: #bbbbbb"> </span><span style="color: #008800; font-style: italic">leaprc</span><span style="color: #bbbbbb"> </span><span style="color: #008800; font-style: italic">文件</span><span style="color: #bbbbbb"> </span> loadamberprep<span style="color: #bbbbbb"> </span>GLYCAM_06_lipids.prep<span style="color: #bbbbbb"> </span><span style="color: #008800; font-style: italic">#</span><span style="color: #bbbbbb"> </span><span style="color: #008800; font-style: italic">加载脂的</span><span style="color: #bbbbbb"> </span><span style="color: #008800; font-style: italic">prep</span><span style="color: #bbbbbb"> </span><span style="color: #008800; font-style: italic">文件</span><span style="color: #bbbbbb"></span> <span style="color: #AA22FF">set</span><span style="color: #bbbbbb"> </span>CHO<span style="color: #bbbbbb"> </span>tail<span style="color: #bbbbbb"> </span>CHO.1.C5<span style="color: #bbbbbb"> </span><span style="color: #008800; font-style: italic">#</span><span style="color: #bbbbbb"> </span><span style="color: #008800; font-style: italic">CHO的尾原子设为</span><span style="color: #bbbbbb"> </span><span style="color: #008800; font-style: italic">C5</span><span style="color: #bbbbbb"></span> <span style="color: #AA22FF">set</span><span style="color: #bbbbbb"> </span>PGL<span style="color: #bbbbbb"> </span>head<span style="color: #bbbbbb"> </span>PGL.1.O1<span style="color: #bbbbbb"> </span><span style="color: #008800; font-style: italic">#</span><span style="color: #bbbbbb"> </span><span style="color: #008800; font-style: italic">PGL的头原子设为</span><span style="color: #bbbbbb"> </span><span style="color: #008800; font-style: italic">O1</span><span style="color: #bbbbbb"></span> <span style="color: #AA22FF">set</span><span style="color: #bbbbbb"> </span>PGL<span style="color: #bbbbbb"> </span>tail<span style="color: #bbbbbb"> </span>PGL.1.C3<span style="color: #bbbbbb"> </span><span style="color: #008800; font-style: italic">#</span><span style="color: #bbbbbb"> </span><span style="color: #008800; font-style: italic">PGL的尾原子设为</span><span style="color: #bbbbbb"> </span><span style="color: #008800; font-style: italic">C3</span><span style="color: #bbbbbb"></span> <span style="color: #B8860B">lipid</span><span style="color: #bbbbbb"> </span><span style="color: #666666">=</span><span style="color: #bbbbbb"> </span>sequence<span style="color: #bbbbbb"> </span><span style="color: #666666">{</span><span style="color: #bbbbbb"> </span>CHO<span style="color: #bbbbbb"> </span>PGL<span style="color: #bbbbbb"> </span>MYR<span style="color: #bbbbbb"> </span><span style="color: #666666">}</span><span style="color: #bbbbbb"> </span><span style="color: #008800; font-style: italic">#</span><span style="color: #bbbbbb"> </span><span style="color: #008800; font-style: italic">生成脂的直链部分</span><span style="color: #bbbbbb"></span> <span style="color: #AA22FF">set</span><span style="color: #bbbbbb"> </span>lipid<span style="color: #bbbbbb"> </span>tail<span style="color: #bbbbbb"> </span>lipid.2.C2<span style="color: #bbbbbb"> </span><span style="color: #008800; font-style: italic">#</span><span style="color: #bbbbbb"> </span><span style="color: #008800; font-style: italic">PGL的尾原子设为</span><span style="color: #bbbbbb"> </span><span style="color: #008800; font-style: italic">C2</span><span style="color: #bbbbbb"></span> <span style="color: #B8860B">lipid</span><span style="color: #bbbbbb"> </span><span style="color: #666666">=</span><span style="color: #bbbbbb"> </span>sequence<span style="color: #bbbbbb"> </span><span style="color: #666666">{</span><span style="color: #bbbbbb"> </span>lipid<span style="color: #bbbbbb"> </span>MY2<span style="color: #bbbbbb"> </span><span style="color: #666666">}</span><span style="color: #bbbbbb"> </span><span style="color: #008800; font-style: italic">#</span><span style="color: #bbbbbb"> </span><span style="color: #008800; font-style: italic">将</span><span style="color: #bbbbbb"> </span><span style="color: #008800; font-style: italic">MY2</span><span style="color: #bbbbbb"> </span><span style="color: #008800; font-style: italic">添加到</span><span style="color: #bbbbbb"> </span><span style="color: #008800; font-style: italic">"lipid"</span><span style="color: #bbbbbb"> </span><span style="color: #008800; font-style: italic">部分</span><span style="color: #bbbbbb"></span> impose<span style="color: #bbbbbb"> </span>lipid<span style="color: #bbbbbb"> </span><span style="color: #666666">{</span>2<span style="color: #666666">}</span><span style="color: #bbbbbb"> </span><span style="color: #666666">{</span><span style="color: #bbbbbb"> </span><span style="color: #666666">{</span>C1<span style="color: #bbbbbb"> </span>C2<span style="color: #bbbbbb"> </span>C3<span style="color: #bbbbbb"> </span>O1<span style="color: #bbbbbb"> </span>163<span style="color: #666666">}</span><span style="color: #bbbbbb"> </span><span style="color: #666666">}</span><span style="color: #bbbbbb"> </span><span style="color: #008800; font-style: italic">#</span><span style="color: #bbbbbb"> </span><span style="color: #008800; font-style: italic">设定扭转角</span><span style="color: #bbbbbb"></span> impose<span style="color: #bbbbbb"> </span>lipid<span style="color: #bbbbbb"> </span><span style="color: #666666">{</span>2<span style="color: #666666">}</span><span style="color: #bbbbbb"> </span><span style="color: #666666">{</span><span style="color: #bbbbbb"> </span><span style="color: #666666">{</span>C2<span style="color: #bbbbbb"> </span>C3<span style="color: #bbbbbb"> </span>O1<span style="color: #bbbbbb"> </span>C1<span style="color: #bbbbbb"> </span>-180<span style="color: #666666">}</span><span style="color: #bbbbbb"> </span><span style="color: #666666">}</span><span style="color: #bbbbbb"> </span><span style="color: #008800; font-style: italic">#</span><span style="color: #bbbbbb"> </span><span style="color: #008800; font-style: italic">PGL</span><span style="color: #bbbbbb"> </span><span style="color: #008800; font-style: italic">&</span><span style="color: #bbbbbb"> </span><span style="color: #008800; font-style: italic">MYR</span><span style="color: #bbbbbb"></span> impose<span style="color: #bbbbbb"> </span>lipid<span style="color: #bbbbbb"> </span><span style="color: #666666">{</span>2<span style="color: #666666">}</span><span style="color: #bbbbbb"> </span><span style="color: #666666">{</span><span style="color: #bbbbbb"> </span><span style="color: #666666">{</span>C3<span style="color: #bbbbbb"> </span>O1<span style="color: #bbbbbb"> </span>C1<span style="color: #bbbbbb"> </span>C2<span style="color: #bbbbbb"> </span>180<span style="color: #666666">}</span><span style="color: #bbbbbb"> </span><span style="color: #666666">}</span><span style="color: #bbbbbb"></span> impose<span style="color: #bbbbbb"> </span>lipid<span style="color: #bbbbbb"> </span><span style="color: #666666">{</span>2<span style="color: #666666">}</span><span style="color: #bbbbbb"> </span><span style="color: #666666">{</span><span style="color: #bbbbbb"> </span><span style="color: #666666">{</span>O4<span style="color: #bbbbbb"> </span>C1<span style="color: #bbbbbb"> </span>C2<span style="color: #bbbbbb"> </span>O1<span style="color: #bbbbbb"> </span>-60<span style="color: #666666">}</span><span style="color: #bbbbbb"> </span><span style="color: #666666">}</span><span style="color: #bbbbbb"> </span><span style="color: #008800; font-style: italic">#</span><span style="color: #bbbbbb"> </span><span style="color: #008800; font-style: italic">设定扭转角</span><span style="color: #bbbbbb"></span> impose<span style="color: #bbbbbb"> </span>lipid<span style="color: #bbbbbb"> </span><span style="color: #666666">{</span>2<span style="color: #666666">}</span><span style="color: #bbbbbb"> </span><span style="color: #666666">{</span><span style="color: #bbbbbb"> </span><span style="color: #666666">{</span>C1<span style="color: #bbbbbb"> </span>C2<span style="color: #bbbbbb"> </span>O1<span style="color: #bbbbbb"> </span>C1<span style="color: #bbbbbb"> </span>-180<span style="color: #666666">}</span><span style="color: #bbbbbb"> </span><span style="color: #666666">}</span><span style="color: #bbbbbb"> </span><span style="color: #008800; font-style: italic">#</span><span style="color: #bbbbbb"> </span><span style="color: #008800; font-style: italic">PGL</span><span style="color: #bbbbbb"> </span><span style="color: #008800; font-style: italic">&</span><span style="color: #bbbbbb"> </span><span style="color: #008800; font-style: italic">MY2</span><span style="color: #bbbbbb"></span> impose<span style="color: #bbbbbb"> </span>lipid<span style="color: #bbbbbb"> </span><span style="color: #666666">{</span>2<span style="color: #666666">}</span><span style="color: #bbbbbb"> </span><span style="color: #666666">{</span><span style="color: #bbbbbb"> </span><span style="color: #666666">{</span>C2<span style="color: #bbbbbb"> </span>O1<span style="color: #bbbbbb"> </span>C1<span style="color: #bbbbbb"> </span>C2<span style="color: #bbbbbb"> </span>180<span style="color: #666666">}</span><span style="color: #bbbbbb"> </span><span style="color: #666666">}</span><span style="color: #bbbbbb"></span> <span style="color: #008800; font-style: italic">#</span><span style="color: #bbbbbb"> </span><span style="color: #008800; font-style: italic">注意上面设定的扭转角数值可能不是最佳值</span><span style="color: #bbbbbb"></span> savepdb<span style="color: #bbbbbb"> </span>lipid<span style="color: #bbbbbb"> </span>DMPC.pdb<span style="color: #bbbbbb"> </span><span style="color: #008800; font-style: italic">#</span><span style="color: #bbbbbb"> </span><span style="color: #008800; font-style: italic">保存</span><span style="color: #bbbbbb"> </span><span style="color: #008800; font-style: italic">pdb</span><span style="color: #bbbbbb"> </span><span style="color: #008800; font-style: italic">文件</span><span style="color: #bbbbbb"></span> saveamberparm<span style="color: #bbbbbb"> </span>lipid<span style="color: #bbbbbb"> </span>DMPC.top<span style="color: #bbbbbb"> </span>DMPC.crd<span style="color: #bbbbbb"> </span><span style="color: #008800; font-style: italic">#</span><span style="color: #bbbbbb"> </span><span style="color: #008800; font-style: italic">保存</span><span style="color: #bbbbbb"> </span><span style="color: #008800; font-style: italic">top</span><span style="color: #bbbbbb"> </span><span style="color: #008800; font-style: italic">和</span><span style="color: #bbbbbb"> </span><span style="color: #008800; font-style: italic">crd</span><span style="color: #bbbbbb"> </span><span style="color: #008800; font-style: italic">文件</span><span style="color: #bbbbbb"></span> </pre></div>