create pure water box for Amber

Download water.pdb .


source leaprc.ff14SB

water=loadpdb water.pdb

solvatebox water SPCBOX(TIP3PBOX) 32

saveAmberParm water water_box.prmtop water_box.inpcrd

the output of water box include 9651 water molecules.

for SPCBOX we need to change charges for that solute water molecule by replacing 

" -1.51973982E+01  7.59869910E+00  7.59869910E+00"


" -1.54452215E+01  7.72261074E+00  7.72261074E+00"


mpirun -np 20 pmemd.MPI -O -i min.mdin -o min.out -c water_box.inpcrd -p water_box.prmtop -r min.rst

mpirun -np 20 pmemd.MPI -O -i heat.mdin -o heat.out -c min.rst -p water_box.prmtop -r heat.rst

mpirun -np 20 pmemd.MPI -O -i md.mdin -o md.out -c heat.rst -p water_box.prmtop -r md.rst -x md.mdcrd