Here is how I installed Dock 6.7 in a local directory on our HPC cluster. I already install MPICH locally, and that is needed to support parallel processing in Dock. This blog post describes installing openMPI, and installing MPICH should install in a similar fashion. Note that Dock 6 does not support openMPI out of the box (though they claim it should be easy to adapt the build to use openmpi instead of MPICH).
Obtain source code
- Step 1. Request License
- Step 2. Download and untar
wget https://dock.compbio.ucsf.edu/dock.6.7_source.tar.gz --no-check-certificate tar -zxvf dock.6.7._source.tar.gz cd dock6/install export MPICH_HOME=/home/eric.kort/jovinge-primary/local
Create a script to equate yacc to bison
The build script expects yacc, even though we are using a GNU build recipe provided by Dock which one might have assumed would use the GNU equivalent, bison. So we need to create a little script that passes all yacc calls to bison. (Thanks to paxdiablo’s answer on stackexhchange. I saved this script to
#! /bin/sh exec '/usr/bin/bison' -y "$@"
Then make it executable
chmod 754 yacc
Now timet o build
make make install make test
Build completed without errors, however I did see some errors on make test. Most worrisome is that the
dock executable could not be found. After some poking around it turns out that when building with cluster support, the exectuable is named
dock.mpi. So let’s create a symlink:
cd ../bin ln -s dock6.mpi dock6
Now most of the tests pass, though there are still some
possible FAILUREs. I am not sure how significant they are, only time will tell. Notably, though, the ligand sampling tutorial ran fine.
For future reference, something like this should be added to .bashrc to tell
dock (and the rest of your ecosystem) where the MPICH executables are: