Linux运行ledock

LeDock,LePro下载地址，下载Linux_x86_64版本，放入指定文件夹，运行命令：

chmod +x ledock_linux_x86
chmod +x lepro_linux_x86

为了运行简单，会把ledock_linux_x86和lepro_linux_x86重命名为ledock、lepro。
lepro的运行参数：
-rot：旋转某条链的残基，使结合位点的主轴与笛卡尔坐标对齐
-metal：保留文件中的离子
-metal -p：保留蛋白中的金属离子的电荷

1. 蛋白处理和参数文件

当前文件下只有蛋白文件xaa.pdb，运行lepro后会生成对接参数文件dock.in、处理后的蛋白文件pro.pdb。

(base) [user@localhost Ledock]$ /home/user/software/ledock/lepro
************************************************************
*      LePro                                               *
*            Add hydrogen atoms to a protein &             *
*            write the input file for LeDock               *
*      Copyright (C) 2013-21 Hongtao Zhao, PhD             *
*      Email: htzhaovv@gmail.com                           *
************************************************************
----------Usage:
          lepro [PDB file] [-rot || -metal || -p]
          -rot  [[chain] resid] align principal axes of the binding site with Cartesian
          -metal keep ZN/MN/CA/MG
          -metal -p redistribute metal charge to protein

(base) [user@localhost Ledock]$ ll
total 460
-rw-rw-r-- 1 user user 467216 Aug  9 21:13 xaa.pdb
(base) [user@localhost Ledock]$ /home/user/software/ledock/lepro xaa.pdb
(base) [user@localhost Ledock]$ ll
total 776
-rw-rw-r-- 1 user user    128 Aug  9 21:13 dock.in
-rw-rw-r-- 1 user user 317071 Aug  9 21:13 pro.pdb
-rw-rw-r-- 1 user user 467216 Aug  9 21:13 xaa.pdb

看看dock.in参数文件的内容，如果熟悉Autodock4、Vina的对接，那么xmin、xmax、ymin、ymax、zmin、zmax就很容易计算，下面命令行中给出了计算方式。

(base) [user@localhost Ledock]$ cat dock.in
Receptor
pro.pdb

RMSD
1.0

Binding pocket
xmin xmax
ymin ymax
zmin zmax
# xmin = center_x - size_x/2 	xmax = center_x + size_x/2
# ymin = center_y - size_y/2 	ymax = center_y + size_y/2
# zmin = center_z - size_z/2 	zmax = center_z + size_z/2

Number of binding poses
20

Ligands list
ligands

END

2. 配体处理

在文件下放入配体文件，用obabel生成对应的mol2文件，并生成一个ligands文件，里面内容是lig.mol2

(base) [user@localhost Ledock]$ obabel ligand.pdb -omol2 -O lig.mol2
(base) [user@localhost Ledock]$ ll
total 784
-rw-rw-r-- 1 user user    128 Aug  9 21:13 dock.in
-rw-rw-r-- 1 user user   2383 Aug  9 21:32 lig.mol2
-rw-rw-r-- 1 user user 317071 Aug  9 21:13 pro.pdb
-rw-rw-r-- 1 user user   1265 Aug  9 21:31 ligand.pdb
-rw-rw-r-- 1 user user 467216 Aug  9 21:13 xaa.pdb
(base) [user@localhost Ledock]$ echo lig.mol2 > ligands
(base) [user@localhost Ledock]$ cat ligands
lig.mol2

3. 运行命令ledock

ledock有两个参数：
ledock dock.in就可直接运行对接命令
ledock -spli dok.file 把对接的pose分隔开，生成单独的文件，在每个分开的配体文件中都有结合能数值

(base) [user@localhost Ledock]$ /home/user/software/ledock/ledock
************************************************************
*       LeDock v1.0                                        *
*       Molecular Docking Software                         *
*       Copyright 2013-21 (C) H. Zhao PhD                  *
*       For academic use only                              *
*       www.lephar.com                                     *
************************************************************
--------Usage:
--------ledock config.file    !docking
--------ledock -spli dok.file !split into separate coordinates

(base) [user@localhost Ledock]$ /home/user/software/ledock/ledock dock.in
(base) [user@localhost Ledock]$ /home/user/software/ledock/ledock -spli lig.dok
(base) [user@localhost Ledock]$ ll ../dock/before15pdb/xaa/FAD-UNK-ledock/
total 876
-rw-rw-r-- 1 user user    149 Aug  9 02:41 dock.in
-rw-rw-r-- 1 user user   2475 Aug  9 02:41 ligand.pdb
-rw-rw-r-- 1 user user      9 Aug  9 02:41 ligands
-rw-rw-r-- 1 user user   1352 Aug  9 02:42 lig_dock001.pdb
-rw-rw-r-- 1 user user   1323 Aug  9 02:42 lig_dock002.pdb
-rw-rw-r-- 1 user user   1323 Aug  9 02:42 lig_dock003.pdb
-rw-rw-r-- 1 user user   1323 Aug  9 02:42 lig_dock004.pdb
-rw-rw-r-- 1 user user   1323 Aug  9 02:42 lig_dock005.pdb
-rw-rw-r-- 1 user user   1323 Aug  9 02:42 lig_dock006.pdb
-rw-rw-r-- 1 user user   1323 Aug  9 02:42 lig_dock007.pdb
-rw-rw-r-- 1 user user   1323 Aug  9 02:42 lig_dock008.pdb
-rw-rw-r-- 1 user user   1323 Aug  9 02:42 lig_dock009.pdb
-rw-rw-r-- 1 user user   1323 Aug  9 02:42 lig_dock010.pdb
-rw-rw-r-- 1 user user   1323 Aug  9 02:42 lig_dock011.pdb
-rw-rw-r-- 1 user user   1323 Aug  9 02:42 lig_dock012.pdb
-rw-rw-r-- 1 user user   1323 Aug  9 02:42 lig_dock013.pdb
-rw-rw-r-- 1 user user   1323 Aug  9 02:42 lig_dock014.pdb
-rw-rw-r-- 1 user user  18551 Aug  9 02:42 lig.dok
-rw-rw-r-- 1 user user   2386 Aug  9 02:41 lig.mol2
-rw-rw-r-- 1 user user 319931 Aug  9 02:41 pro.pdb

4. 辅因子

教程中指出有些时候我们对接时需要保留一些辅因子、水分子、金属离子。可以把原始pdb文件中保留的分子复制到 pro.pdb中，并把保留分子的 ”HETATM“ 改为 ”ATOM“。这种小分子确少氢原子不会显著影响对接结果。
原文：

In some cases, cofactor, metal or a few water molecules are important for docking. 
If so, one can manually copy the coordinates of such molecules from the original PDB into pro.pdb
and change “HETATM” to “ATOM”. 
Missing hydrogen atoms for such small molecules shall not significantly influence the docking outcome.