基于结构的虚拟筛选模型 gnina 从源码编译

原作者也提供了Docker

docker pull gnina/gnina

所需要的所有文件：

链接: https://pan.baidu.com/s/1HElF1sdx4a0xYJ4OBbe5lA
密码: tliv

安装 CUDA

刚开始有个很长的文字，要按一堆enter才能往下的，直接ctrl+c就可以跳过
接下来，
第一个，回答accept
第二个，要你装驱动的选择，回答n，不装
下面全都回答 y

sudo sh cuda_10.0.130_410.48_linux.run
sudo vim ~/.bashrc

在 ~/.bashrc 文件最后加上

export PATH=/usr/bin:/usr/local/cuda-10.0/bin${PATH}
export LD_LIBRARY_PATH=/usr/local/cuda-10.0/lib64:${LD_LIBRARY_PATH}

source ~/.bashrc

安装 cudnn

sudo cp -rp cuda/include/cudnn.h /usr/local/cuda-10.0/include
sudo cp -rp cuda/lib64/libcudnn* /usr/local/cuda-10.0/lib64
sudo chmod a+r /usr/local/cuda-10.0/include/cudnn.h /usr/local/cuda-10.0/lib64/libcudnn*

重启

nvcc -V

zdx@wood:~$ nvcc -V
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2018 NVIDIA Corporation
Built on Sat_Aug_25_21:08:01_CDT_2018
Cuda compilation tools, release 10.0, V10.0.130

安装依赖

sudo apt-get install build-essential cmake git wget libboost-all-dev libeigen3-dev libgoogle-glog-dev libprotobuf-dev protobuf-compiler libhdf5-dev libatlas-base-dev python3-dev librdkit-dev python3-numpy python3-pip python3-pytest

编译 Openbabel 3

cd openbabel
mkdir build
cd build
cmake -DWITH_MAEPARSER=OFF -DWITH_COORDGEN=OFF -DPYTHON_BINDINGS=ON -DRUN_SWIG=ON ..
make -j8
sudo make install

编译libmolgrid

cd libmolgrid
mkdir build
cd build
cmake ..
make -j8
sudo make install

编译 gnina

cd gnina
mkdir build
cd build
cmake ..
make -j8
sudo make install