DOCK 3.8 testing on C7

These are instructions to follow on Cluster 7 to run DOCK 3.8.

• step 1. log in to C7
• cd hdd02 # find a place to work
• mkdir docking # create an area for docking
• cd docking
• pwd

/nfs/home/xyz/hdd02/docking

• screen -S john # could also be tmux

1. set up a docking environment on C7

module load dock
echo $DOCK_INSTALL_PATH
echo $DOCKBASE

1. copy test data to my account

cp -r ${DOCK_INSTALL_PATH}/test/docking  test
cd test

1. edit file to point to my own copy

./test_subdock.sh

After copying the test directory into your own workspace, edit test_subdock.sh so it uses the local copied directory. Change this line:

find test_ligs -name '*.db2.tgz' -exec realpath {} \; > ${DOCK_INSTALL_PATH}/test/docking/split_database_index

to:

find test_ligs -name '*.db2.tgz' -exec realpath {} \; > split_database_index

Change these:

export EXPORT_DEST="${DOCK_INSTALL_PATH}/test/docking/output"
export INPUT_SOURCE="${DOCK_INSTALL_PATH}/test/docking/split_database_index"
export DOCKFILES="${DOCK_INSTALL_PATH}/test/docking/dockfiles"

to:

export EXPORT_DEST="$(pwd)/output"
export INPUT_SOURCE="$(pwd)/split_database_index"
export DOCKFILES="$(pwd)/dockfiles"