How to compile AutoDock Vina from source code? - c++

Question

I am trying to compile a program called AutoDock Vina from this web site: http://vina.scripps.edu/manual.html#build. I can't use prebuilt binaries files directly because I have to change some parameters in the source code.
I installed build-essential, g++ and boost. I downloaded autodock_vina_1_1_2.tgz and unpacked.
I tried to follow instructions in the site but I failed. I changed Makefile in the autodock_vina_1_1_2/build/linux/debug/Makefile:
BASE=/usr/lib/python2.7/dist-packages/
BOOST_VERSION=1.67.0
BOOST_INCLUDE = $(BASE)/include
C_PLATFORM=-static -pthread
GPP=/usr/bin/g++
C_OPTIONS= -g
BOOST_LIB_VERSION=
include ../../makefile_common
Note: I also tested BASE=/usr or /usr/libexec or any logic combination according to the installation information above
And then when make I encounter this error message:
(base) root#kali:~/Desktop/share/autodock_vina_1_1_2/build/linux/debug# make
/usr/bin/g++ -static -pthread -ansi -Wno-long-long -g -I /usr/lib/python2.7/dist-packages//include -I ../../../src/lib -o main.o -c ../../../src/main/main.cpp
In file included from /usr/include/boost/assert.hpp:58,
from /usr/include/boost/random/uniform_smallint.hpp:22,
from /usr/include/boost/random.hpp:86,
from ../../../src/lib/random.h:26,
from ../../../src/lib/quaternion.h:30,
from ../../../src/lib/conf.h:28,
from ../../../src/lib/tree.h:26,
from ../../../src/lib/model.h:29,
from ../../../src/lib/parse_pdbqt.h:26,
from ../../../src/main/main.cpp:33:
../../../src/lib/quaternion.h: In function ‘void quaternion_normalize(qt&)’:
../../../src/lib/quaternion.h:79:9: error: ‘quaternion_is_normalized’ was not declared in this scope; did you mean ‘quaternion_normalize’?
79 | assert(quaternion_is_normalized(q));
| ^~~~~~~~~~~~~~~~~~~~~~~~
../../../src/lib/quaternion.h: In function ‘void quaternion_normalize_approx(qt&, fl)’:
../../../src/lib/quaternion.h:91:16: error: ‘quaternion_is_normalized’ was not declared in this scope; did you mean ‘quaternion_normalize’?
91 | assert(quaternion_is_normalized(q));
| ^~~~~~~~~~~~~~~~~~~~~~~~
../../../src/main/main.cpp: In function ‘path make_path(const string&)’:
../../../src/main/main.cpp:50:44: error: no matching function for call to ‘boost::filesystem::path::path(const string&, bool (&)(const string&))’
So, how can I compile AutoDock Vina from source code?

Answer 1

You don't need to "make". Just move files into bin folder apply these instructions:
$ cd Downloads/
$ wget http://mgltools.scripps.edu/downloads/tars/releases/REL1.5.6/mgltools_x86_64Linux2_1.5.6.tar.gz
$ wget http://vina.scripps.edu/download/autodock_vina_1_1_2_linux_x86.tgz
#install python PIL:
#install libjpeg62
$ sudo apt-get install libjpeg62:i386
#download Autodock4 and AutoGrid4
$ sudo wget http://autodock.scripps.edu/downloads/autodock-registration/tars/dist426/autodocksuite-4.2.6-x86_64Linux2.tar
Installation:
Now that we have the tar files in the Downloads folder, we will extract and install them one by one. Let’s install AutoDock suite first, then later the MGL tools, and AutoDock Vina. To install them, open the terminal and go to the Downloads folder again.
$ cd Downloads
$ tar xvf autodocksuite-4.2.6-x86_64Linux2.tar
$ cd x86_64Linux2
$ sudo mv autodock4 /usr/local/bin
$ sudo mv autogrid4 /usr/local/bin
#install mgltools:
$ cd Downloads
$ tar xvzf mgltools_x86_64Linux2_1.5.6.tar.gz
$ cd mgltools_x86_64Linux2_1.5.6
$ ./install.sh