What are some free programs to do docking? 
https://mattermodeling.stackexchange.com/questions/1790/what-are-some-free-programs-to-do-docking

Megadock 4.o
https://www.bi.cs.titech.ac.jp/megadock/usage.html



https://www.bi.cs.titech.ac.jp/megadock/usage.html
(d) CPU single node
$ ./megadock -R data/receptor.pdb -L data/ligand.pdb



1. Install FFW3 (https://www.bi.cs.titech.ac.jp/megadock/faq.html ->  4. How to install FFTW3?)
-------------------
	download fftw3_3.3.8.orig.tar.gz (https://www.fftw.org/)
	tar xvf fftw3_3.3.8.orig.tar.gz
	cd fftw-3.3.8
	./configure --enable-float --enable-sse2 --prefix=/usr/local   	# I used this one
  	(--enable-sse, --enable-sse2 or --enable-avx option enable the compilation of SIMD core for SSE, SSE2 		or AVX, respectively.)
  	(if you use intel compiler, add the option "CC=icc".)
	sudo make
	sudo make check
	sudo make install 
	sudo make installcheck    	
	Note: The FFT package will be installed on path /usr/local

	
2. From Build.md file at doc dir. (https://www.bi.cs.titech.ac.jp/megadock/usage.html -> click Download at top menu)
	## Compile (d): CPU single node (only thread parallelization)

	tar xvf megadock-4.1.1.tgz
	cd megadock-4.1.1
	Note: I have g++


	### 2. Edit Makefile
	FFTW_INSTALL_PATH ?= /usr/local
	CPPCOMPILER       ?= g++
	OPTIMIZATION      ?= -O3
	OMPFLAG           ?= -fopenmp

	USE_GPU := 0
	USE_MPI := 0


	### 3. Compile
	make
	binary file `megadock` will be generated.
	
	### 3. Run
	./megadock --help
	mkdir _Vim_Ann
	cd _Vim_Ann
	nohup time ../megadock -R Vimentin.pdb -L Annexin_A2.pdb -o vim_ann.out -O -N 5 1>log.out 2>&1 &
	tail -f  log.out 
	
	### 4. Results will be (in 3 files):
	vim_ann.csv  
	vim_ann.detail  
	vim_ann.out 
	
	### 5. decoygen (https://www.bi.cs.titech.ac.jp/megadock/usage.html) "o generate decoy pdbfiles"
	
	- to generate 1st ranked decoy
	
	../decoygen Annexin_A2.1.pdb Annexin_A2.pdb vim_ann.out 1
 	cat Vimentin.pdb Annexin_A2.1.pdb > vim_ann.1.pdb
 	
 	- to generate all decoys
 	
 	i=1; cat vim_ann.out| while read LINE; do ../decoygen Annexin_A2..pdb Annexin_A2.pdb vim_ann.out $i; cat Vimentin.pdb Annexin_A2..pdb > vim_ann..pdb; let i=$i+1; done
 	
 	end-of-document