linux下ZDOCK与ZRANK安装及基础使用方法

ZDOCK: Performs a full rigid-body search of docking orientations between two proteins.
ZRANK: A docking refinement program developed to provide fast and accurate rescoring of models from initial-stage docking (e.g. from ZDOCK), as well as refined docking models (e.g. from RosettaDock).

下载

ZDOCK官网：https://zlab.umassmed.edu/zdock/
使用non-profit email address下载
得到如下文件：
ZDOCK并行版：zdock3.0.2_linux_mpi.tar.gz
ZRANK：zrank2_linux.tar.gz

安装

ZDOCK解压即用

tar -zxvf zdock3.0.2_linux_mpi.tar.gz

出现 libg2c.so.0:cannot open shared object file：
解决方法参考：https://blog.csdn.net/wujiaqi168/article/details/17055543
ubuntu下载Fedora，可手动添加到~/.bashrc中export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/path/to/libg2c.so.0

出现 libmpi.so.0:cannot open shared object file：
解决方法：可能在/usr/lib或/usr/lib64下，或者openmpi的lib里，添加至LD_LIBRARY_PATH即可，没有的话用ln -s把.so添加软链到.so.0即可

ZRANK解压即用

tar -zxvf zrank2_linux.tar.gz

添加变量方便调用，zrank文件也就放一块了

export ZDOCK=/path/to/ZDOCK

使用

对接
cp $ZDOCK/uniCHARMM ./
$ZDOCK/mark_sur receptor.pdb receptor_m.pdb #pdb preprocess
$ZDOCK/mark_sur ligand.pdb ligand_m.pdb
$ZDOCK/block.pl receptor_m.pdb block_resi.list > receptor_m_blocked.pdb #block_resi.list给出先验知识中不参与互作的残基，a file with one number per line
nohup mpiexec --host "localhost:12" $ZDOCK/zdock -R receptor_m_blocked.pdb -L ligand_m.pdb -o zdock.out -N 54000 -D & #mpi run 12core on localhost

-D进行6度精细采样。Decoy sets are available for 6 degree sampling (54000 predictions per test case) and 15 degree sampling (3600 predictions per test case), for several ZDOCK versions. It is recommended, though not necessary, to use 6 degree sampling for the ZDOCK runs (“-D” option in ZDOCK) as this provides more hits and thus provides optimal input for ZRANK.
输出文件的格式含义：（参考http://blog.sina.com.cn/s/blog_15d0344a30102xeh8.html）
从中可以看出ZDOCK仅记录了对接结果中蛋白之间的角度和位置，并没有残基间的信息，是很粗糙的构象搜索，可以的话后续应进行Local refinement（例如配合rosetta）

创建对接结果
mkdir ./docking_results
head -n 105 ./zdock.out > ./docking_results/zdock_t100.out
cd ./docking_results
cp ../receptor_m.pdb ./
cp ../ligand_m.pdb ./
cp $ZDOCK/create_lig ./
$ZDOCK/create.pl zdock_t100.out

加氢并用ZRANK打分（用ROSETTA）
mkdir ./zrank_results
head -n 105 ./zdock.out > ./zrank_results/zdock_t100.out
cd ./zrank_results
cp ../receptor_m.pdb ./
cp ../ligand_m.pdb ./
mkdir ./outdir_1
mpirun -n 2 $ROSETTA/main/source/bin/score.mpi.linuxgccrelease -in:file:s receptor_m.pdb -no_optH false -output #用ROSETTA score protocol快速简单加氢，只需要加氢后的pdb文件
mv ./outdir_1/receptor_m_0001.pdb ./receptor_m.pdb.h
mpirun -n 2 $ROSETTA/main/source/bin/score.mpi.linuxgccrelease -in:file:s ligand_m.pdb -no_optH false -output 
mv ./outdir_1/ligand_m_0001.pdb ./ligand_m.pdb.h
#修改zdock_t100.out中为新pdb文件后
$ZDOCK/zrank zdock_t100.out 1 100