#!/bin/tcsh

echo off

foreach file(*pdb)
 #       cp $file temp.pdb
	setenv pref1 `echo $file | sed 's/.pdb//'`
cat <<eof > $pref1.leap
source leaprc.ff03
$pref1 = loadpdb $pref1.pdb
saveAmberParm $pref1 $pref1.prmtop $pref1.prmcrd
quit
/
eof
     
       /projects/Biogroup/AMBER/amber9/exe/tleap -f $pref1.leap

cat <<eof > $pref1-min.in
# 200 steps of minimization, generalized Born solvent model 
&cntrl
maxcyc=200, ncyc=1, imin=1, cut=12.0, igb=1, ntb=0, ntpr=1,
/
eof

 /projects/Biogroup/AMBER/amber9/exe/sander -i $pref1-min.in -o $pref1.min1.out -c $pref1.prmcrd -p $pref1.prmtop -r $pref1.min1.xyz

#rm -f $pref1.leap $pref1.min1.out $pref1.prmtop $pref1.prmcrd mdinfo leap.log $pref1-min.in
rm -f $pref1.leap mdinfo leap.log $pref1-min.in



end
