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CADD课程学习(7)-- 模拟靶点和小分子相互作用 (柔性对接 AutoDock)
2022-07-06 04:16:00 【发呆的比目鱼】
CADD课程学习(7)-- 模拟靶点和小分子相互作用 (柔性对接 AutoDock)
半柔性对接VS柔性对接
半柔性
- A utodockTools配体、受体文件准备:
①删水加H原子、加电荷、合并非极性氢、设置配体可旋转键;
②保存lig.pdbqt和rec.pdbqt; - AutoGrid格点计算:
①选择rec.pdbqt,设置探针原子类型,设置盒子大小和位置;
②保存dock.gpf运行AutoGrid程序计算格点,输出dock.glg; - AutoDock对接计算:
①选择lig.pdbqt和rec.pdbqt,设置构象搜索;
②保存dock.dpf,运行AutoDock程序计算格点,输出dock.dlg;
柔性 - Autodock Tools配体、受体文件准备:
①删水加H原子、加电荷、合并非极性氢、设置配体可旋转键;
②保存lig.pdbqt、rec rigid.pdbqt和rec_flex.pdbqt; - AutoGrid格点计算:
①选择rec_rigid.pdbqt,设置探针原子类型,设置盒子大小和位置;
②保存dock.gpf,运行AutoGrid程序计算格点,输出dock.glg;工 - AutoDock对接计算:
①选择lig.pdbqt、rec rigid.pdbqt和rec_flex.pdbqt设置受体柔性残基可旋转键,设置构象搜索;
②保存dock.dpf,运行AutoDock程序计算格点,输出dock.dlg
生成格点:.\autogrid4.exe -p .\dockflex.gpf
命令行: .\autodock4.exe -p .\dockflex.dpf
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