# Not the part of distribution
# create directory wrk_dir, with UHBD readable pdb files in its 
# pdbs/ subdirectory, place pdb file name list to the file "pdbnames" there

./do_pipsa_UHBD_prep /home/ra/gabdoull/wrk/pipsa/ /home/ra/gabdoull/wrk/pipsa/PH/ 

# this will generate /home/ra/gabdoull/wrk/pipsa/PH/uhbd/ 
# use pdb file names from /home/ra/gabdoull/wrk/pipsa/PH/pdbs/pdbnames
# and generate the files needed for uhbd calculations ("names" with protein names, and uhbd.in)

./do_pipsa_UHBD_chk /home/ra/gabdoull/wrk/pipsa/ /home/ra/gabdoull/wrk/pipsa/PH/uhbd /home/ra/gabdoull/wrk/pipsa/bin/uhbd
./do_pipsa_UHBD_grids /home/ra/gabdoull/wrk/pipsa/ /home/ra/gabdoull/wrk/pipsa/PH/uhbd /home/ra/gabdoull/wrk/pipsa/bin/uhbd

# this will compute elec potentials in  /home/ra/gabdoull/wrk/pipsa/PH/uhbd/
# calculate similarity matrix and derivatives for grids in  /home/ra/gabdoull/wrk/pipsa/PH/uhbd/:

./do_pipsa_sim /home/ra/gabdoull/wrk/pipsa/ /home/ra/gabdoull/wrk/pipsa/PH/uhbd/

# phylip diagrams can be generated using the script 

./do_pipsa_phylip /home/ra/gabdoull/wrk/pipsa/ /home/ra/gabdoull/wrk/pipsa/PH/uhbd/ /home/ra/gabdoull/wrk/pipsa_add/phylip/


./do_pipsa_UHBD_prep /home/ra/gabdoull/wrk/pipsa/ /home/ra/gabdoull/wrk/pipsa/WW
./do_pipsa_APBS_prep /home/ra/gabdoull/wrk/pipsa/ /home/ra/gabdoull/wrk/pipsa/WW
./do_pipsa_UHBD_chk /home/ra/gabdoull/wrk/pipsa/ /home/ra/gabdoull/wrk/pipsa/WW/uhbd /home/ra/gabdoull/wrk/pipsa/bin/uhbd
./do_pipsa_UHBD_grids /home/ra/gabdoull/wrk/pipsa/ /home/ra/gabdoull/wrk/pipsa/WW/uhbd /home/ra/gabdoull/wrk/pipsa/bin/uhbd
./do_pipsa_APBS_grids  /home/ra/gabdoull/wrk/pipsa/  /home/ra/gabdoull/wrk/pipsa/WW/apbs/ /home/ra/gabdoull/progs/apbs/bin/i686-pc-linux/apbs 
./do_pipsa_sim /home/ra/gabdoull/wrk/pipsa/ /home/ra/gabdoull/wrk/pipsa/WW/uhbd/
./do_pipsa_sim /home/ra/gabdoull/wrk/pipsa/ /home/ra/gabdoull/wrk/pipsa/WW/apbs/

./do_pipsa_UHBD_prep /home/ra/gabdoull/wrk/pipsa/ /home/ra/gabdoull/wrk/pipsa/PH
./do_pipsa_APBS_prep /home/ra/gabdoull/wrk/pipsa/ /home/ra/gabdoull/wrk/pipsa/PH
./do_pipsa_UHBD_chk /home/ra/gabdoull/wrk/pipsa/ /home/ra/gabdoull/wrk/pipsa/PH/uhbd /home/ra/gabdoull/wrk/pipsa/bin/uhbd
./do_pipsa_UHBD_grids /home/ra/gabdoull/wrk/pipsa/ /home/ra/gabdoull/wrk/pipsa/PH/uhbd /home/ra/gabdoull/wrk/pipsa/bin/uhbd
./do_pipsa_APBS_grids  /home/ra/gabdoull/wrk/pipsa/  /home/ra/gabdoull/wrk/pipsa/PH/apbs/ /home/ra/gabdoull/progs/apbs/bin/i686-pc-linux/apbs 
./do_pipsa_sim /home/ra/gabdoull/wrk/pipsa/ /home/ra/gabdoull/wrk/pipsa/PH/uhbd/
./do_pipsa_sim /home/ra/gabdoull/wrk/pipsa/ /home/ra/gabdoull/wrk/pipsa/PH/apbs

./do_pipsa_APBS_grids  /home/ra/gabdoull/wrk/pipsa/ /home/ra/gabdoull/wrk/pipsa/WW/apbs/ /home/ra/gabdoull/progs/apbs/bin/i686-pc-linux/apbs 
./do_pipsa_UHBD_grids  /home/ra/gabdoull/wrk/pipsa/ /home/ra/gabdoull/wrk/pipsa/WW/uhbd/ /home/ra/gabdoull/wrk/pipsa/bin/uhbd
./do_pipsa_sim /home/ra/gabdoull/wrk/pipsa/ /home/ra/gabdoull/wrk/pipsa/WW/apbs/
./do_pipsa_sim /home/ra/gabdoull/wrk/pipsa/ /home/ra/gabdoull/wrk/pipsa/WW/uhbd/
./do_pipsa_sim /home/ra/gabdoull/wrk/pipsa/ /home/ra/gabdoull/wrk/pipsa/WW/grid/

