DOCK

DOCK is a free program used for modeling the binding modes of small molecule (such as drug molecule) within the active site(s) of macromolecule or receptor.

• Who distributes the software? Kuntz group in University of California (UCSF)
• Version: 6.2, released in the March of 2008.
• Availability: tork.ncifcrf.gov, Small Blade Center
• Compilers Used: GCC Version 4.1.2
• Home Directory: /opt/nasapps/stow/dock6

  Please note that parallel version of DOCK and other utility programs were compiled using mpich2 (/opt/nasapps/build/MPI-GCC/MPICH2-1.0.7/), and has a suffix "mpi". For example, dock6.mpi is the parallel version of dock. dock6 is the serial version.

• To run any parallel dock software, users have to do the following:

  // setup variables/path for mpich2 and DOCK
  
     setenv DOCKHOME /opt/nasapps/stow/dock6/bin/
     setenv MPICHHOME /opt/nasapps/build/MPI-GCC/MPICH2-1.0.7
     set path = ($MPICHHOME/bin $DOCKHOME/bin $path)
  // start mpd
   mpd &
  
  // mpirun from $MPICHHOME/bin and dock6.mpi is a link from
  // /opt/nasapps/bin to  /opt/nasapps/stow/dock6/bin/dock6.mpi
   mpirun -np 2 dock6.mpi -i mpi.dockin -o mpi.dockmpiout
  
  // cleanup with mpdallexit
     mpdallexit
  

• Contact Info: foleyd@ncifcrf.gov sravi@ncifcrf.gov