loadAmberParams frcmod.ionsjc_tip3p
source leaprc.ff14SB
loadAmberParams frcmod.ions1lsm_1264_tip3p
# Load the PDBs
1e0q = loadPDB tmp.pdb
relax 1e0q

# Solvate
solvateBox 1e0q TIP3PBOX 20
set 1e0q box {70 70 70}
#Add ions

addIonsRand 1e0q NA 0
addIonsRand 1e0q CL 0

# Save topology files
saveAmberParm 1e0q 1e0q_box.prmtop 1e0q_box.inpcrd

# Quit
quit
~   

#!/bin/bash
rm tmp*
for i in $(ls *.pdb)
do
rm tmp*
name=`echo $i|awk 'BEGIN{FS=".";}{print $1;}'`
echo $name
if grep -q "^MODEL" $i
  then
    pdb4amber --noter --model=1 -d -p -i $i -o tmp6.pdb 2>$name.log
  else
    awk '($5 == "A" || $5 =="1") && $1=="ATOM" { print $0}' $i >tmp7.pdb
    pdb4amber --noter -d -p -i tmp7.pdb -o tmp6.pdb 2>$name.log
fi
#awk '$5 == "A" && $1=="ATOM" { print $0}' $i >tmp6.pdb

#pdb4amber --noter -d -p -i tmp6.pdb -o tmp5.pdb
sed "s/HIS/HIE/g" tmp6.pdb >tmp4.pdb
#reduce -Trim tmp4.pdb>tmp3.pdb

if grep -q "H3" tmp4.pdb
   then
   echo "H3 found"
   cat tmp4.pdb|grep ATOM >tmp1.pdb
   else
   echo "NO H3,adding hydrogen"
   reduce -BUILD tmp4.pdb>tmp2.pdb 2>>$name.log
   cat tmp2.pdb|grep ATOM >tmp1.pdb
fi
sed -i '/H1/d' tmp1.pdb
sed -i '/H2/d' tmp1.pdb

sed -n '/H3/p' tmp1.pdb|sed 's/H3  [A-Z][A-Z][A-Z]/C   ACE/g' >tmp_b
sed -n '/OXT/p' tmp1.pdb|sed 's/OXT [A-Z][A-Z][A-Z]/N   NME/g' >tmp_e

if ! [ -s tmp_b ];then echo "$i ACE failed";exit;fi
if ! [ -s tmp_b ];then echo "$i NME failed";exit;fi

sed -i '$d' tmp1.pdb
sed -i '/H3/d' tmp1.pdb
sed -i '/OXT/d' tmp1.pdb
cat tmp_b tmp1.pdb tmp_e>tmp.pdb
sed -i '$a\END' tmp.pdb
sed "s/1e0q/$name/g" tleap.in >${name}_tleap.in
echo "tleaping..."
tleap -f ${name}_tleap.in 2>&1 >>$name.log
x=`grep "box size" $name.log |awk '{print $5}'`
y=`grep "box size" $name.log |awk '{print $6}'`
z=`grep "box size" $name.log |awk '{print $7}'`
x_int=`printf '%.0f' $x`
y_int=`printf '%.0f' $y`
z_int=`printf '%.0f' $z`
x_format=`printf '%.*f' 7 $x_int`
y_format=`printf '%.*f' 7 $y_int`
z_format=`printf '%.*f' 7 $z_int`
sed -i '$d' ${name}_box.inpcrd
echo "  $x_format  $y_format  $z_format  90.0000000  90.0000000  90.0000000">>${name}_box.inpcrd
echo "minimizing......"
mpirun -np 10 pmemd.MPI -O -i min.mdin -o ${name}_min.out -c ${name}_box.inpcrd -p ${name}_box.prmtop -r ${name}_min.rst
echo "heating......"
mpirun -np 10 pmemd.MPI -O -i heat.mdin -o ${name}_heat.out -c ${name}_min.rst -p ${name}_box.prmtop -r ${name}_heat.rst
echo "waiting for last simulation to finish...."
result=`checkRunningProcess.sh pmemd.cuda.MPI`
until [ $result == "NR" ];
do
sleep 10
result=`checkRunningProcess.sh pmemd.cuda.MPI`
done
echo "production running......"
mpirun -np 2 pmemd.cuda.MPI -O -i md.mdin -o ${name}_md.out -c ${name}_heat.rst -p ${name}_box.prmtop -r ${name}_md.rst -x ${name}_md.mdcrd &