debanjansen48
commented
4 years ago One more thing. How can I setup virtual screening process using AUTODOCK GPU? can i dock multiple ligands (300k) with multiple protein target (with defined binding site,) as well ligands with more then 25 torsion with this tool??
As I found for few sets of ligand AutoDock cant perform whereas DNIC server can perform the same. I have enough experimental evidences that large molecules bind with certain receptor and produce activity. But AutoDock4 or Vina unable to perform docking. Software like DNIC (http://dinc.kavrakilab.org/ ) or PLANTS, R-Dock can dock them. In this case AutoDock GPU is useful ??
L30nardoSV
I am using CUDA supported GPU RTX2080. After retrieving files from GIT , extracted and entered in src folder (Downloads/gpuautodock/src/autodock-4.0.1). issued command ./configure returns
checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking for gawk... (cached) gawk checking for g++... g++ checking for C++ compiler default output file name... a.out checking whether the C++ compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking for style of include used by make... GNU checking dependency style of g++... gcc3 checking for a BSD-compatible install... /usr/bin/install -c checking for ranlib... ranlib checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking dependency style of gcc... gcc3 checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for size_t... yes checking whether struct tm is in sys/time.h or time.h... time.h checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for gethostname... yes checking for pow... no checking for sqrt... no checking for strncasecmp... yes configure: creating ./config.status config.status: creating Makefile config.status: executing depfiles commands
now issued the command "make" returns
~/Downloads/gpuautodock/src/autodock-4.0.1$ make
make: Nothing to be done for 'all'.
my os id LinuxMint 2019.2