#### PBS script set up to do AutoDock Run April 2003
#### Ravi Email: sravi@ncifcrf.gov 
####--------------------------------------------------------------------
####               READ  THIS FIRST
#### This assumes that you have already ran the script 
#### prepare_for_pbs and your user-account is located in 
#### /users/class/username 
#### If  your username is located under a different tree
#### Please change the correct pathname in the environment
#### variable "HOM" 
#### It also assumes that there exists a sub-directory "Results"
#### where the final results will be copied to. So make sure you 
#### create a sub-directory called "Results" before you fire this script!
####--------------------------------------------------------------------

#PBS -S /bin/csh -N ADTRUN1
#PBS -l pcput=1:00:00,cput=1:00:20,pvmem=400mb,ncpus=1
#PBS -m e -c c

echo "Started  " `date`

# Prel settings

setenv procid     $$
setenv APPHOM  /usr/local/fbscapp
setenv HOM     /users/class/${USER}
setenv tmpdir    /usr/tmp/${USER}/$procid


# AutoDock Settings

setenv ADHOM /usr/local/fbscapp/autodockroot
setenv AUTODOCK_UTI $ADHOM/dist305/share
set path = ($path $ADHOM/dist305/bin \
                  $ADHOM/dist305/share )

# Clear off all the files and directories

if ( -d $tmpdir ) then
   cd $tmpdir
   rm -fr *
else
   mkdir -p $tmpdir
      if ( -d $tmpdir ) then
           cd $tmpdir
      else
         echo "Problem in making $tmpdir "
         exit
      endif
endif

cp $HOM/Prot.gpf .
cp $HOM/lig.Prot.dpf .
cp $HOM/Prot.pdbqs .
cp $HOM/lig.out.pdbq .

autogrid3 -p Prot.gpf -l Prot.glg

#output files *.map, *.fld, *.pdbqs *.out.pdbq 
#output *.glg *dlg

autodock3 -p lig.Prot.dpf -l lig.Prot.dlg  
get-docked lig.Prot.dlg

cp * $HOM/Results 

cd ./..

rm -fr $tmpdir

echo "Done  " `date`

# TO RUN PBS on NCIIRIS (AutoDock)
# RAVI--April, 2003