写在前面
Autodock Vina作为经典的分子对接工具，上手也比较容易，最近学习了一下，特此记录。
Requirement
- Pymol
2.Plugin ‘GetBox-PyMOL-Plugin’
3.ADFR
4.Autodock Vina
Installation
#源码下载和安装
#Vina
https://vina.scripps.edu/downloads/
export PATH=$PATH:/path/to/your/bin # 添加环境变量
source ~/.bashrc #使生效
#ADFR
https://ccsb.scripps.edu/adfr/downloads/
Prerequisites
1. Pymol in windows
1.1 fetch 7S1S
1.2 删除水分子 'remove resn HOH' / 'A-remove waters'【如果是预测的结构，不需要去除水分子】
1.3 如果结构是多条链的话，删除不关注的链，此时删除B链，'remove chain B'
1.4 pymol中检查结合位点是否有氨基酸突变或缺失
1.5 使用getbox来获取口袋参数。【详见ref2】
#获得的口袋参数如下
--center_x -31.9 --center_y -43.7 --center_z -7.1 --size_x 2
5.8 --size_y 29.8 --size_z 20.6
1.6 删除完所有的小分子配体，并保存结构
remove resn MTA+85k
save 7S1S_pro.pdb
2. ADFR in Linux
给受体结构加氢质子化，reduce包包含在ADFR程序中。
reduce 7S1S_pro.pdb > 7S1S_H.pdb
Prepare_receptor 将受体结构的PDB格式转换成PDBQT格式。
prepare_receptor -r 7S1S_H.pdb -o 7S1S_H.pdbqt
对接参数文件准备，将参数写入txt中，并命名为7S1S_vina.txt
center_x = -31.9
center_y = -43.7
center_z =-7.1
size_x = 25.8
size_y = 29.8
size_z = 20.6
使用Vina进行对接计算。
vina --receptor 7S1S_H.pdbqt --ligand 7s1s_C_MTA.pdbqt --cpu 16 --config 7S1S_vina.txt --out 7S1S_23A_vinaout &
会有九个文件生成，打分最低的即为排名最高的构象。
3. Results
先在linux中转换格式。
babel -ipdbqt 7s1s_C_MTA_out.pdbqt -osdf 7s1s_vina_out.sdf
将对接后的'sdf'文件和原始的结构文件'7s1s.pdb'一起载入pymol中，其中排名第一的构象和试验解出来的构象十分一致，证明Vina的结果有很高的可靠性。
Tips： How to obtain a correct Mol2 file?
Please, note that the Mol2 files submitted to SwissDock should contain all the hydrogen atoms of the molecule.
First of all, try the Mol2 file you already have. Most of the Mol2 files will work, whatever their origin. If one fails, you can try one of the following:
- get it from the ZINC Database if the molecule is already known,
- or, if the molecule comes from a PDB file (e.g. a ligand), you can use the UCSF chimera visualization software to open the PDB file, remove all molecules except the one of interest, add hydrogen atoms (using the Tools/Structure Editing/AddH menu), and save it as a Mol2 file,
- or use openbabel to convert a correct 3D file from another format into the Mol2 format,
- or draw the molecule in 2D in Chemaxon Marvin Sketch (free), add hydrogens, generate 3D coordinates and save the molecule in the "Tripos Mol2 (mol2)" format.
This list is not exhaustive. If you have trouble getting a working Mol2 file, please contact us.
Citations
1.https://blog.csdn.net/MurphyStar/article/details/132708694
2.https://github.com/MengwuXiao/GetBox-PyMOL-Plugin/tree/master
3.https://ccsb.scripps.edu/adfr/downloads/
4.https://www.swissdock.ch/howtomol2.php
