#load force field

include "loadff.inc"

#load the IL box

loadmsf step6_equil_npt.msf

tell boxsize

type=tetr

a=$boxa

b=$boxa

c=$boxa*3

nstepmini=200

#load raw solvent box unit prepared

loadmsf file="waterbox.msf"

tell box

lunit=$boxA

#compute number of replication for each dimmension

nx=int(($a+8)/$lunit+1)

ny=int(($b+8)/$lunit+1)

nz=int(($c+8)/$lunit+1)

#do replication

echo -hs "| building box ..."

replicate nx=$nx ny=$ny nz=$nz stride=($lunit,$lunit,$lunit)

#move center to origin

atom transto pos=(0,0,0) select=all

tell center select=all

#setup crystal/pbc box

crystal type=$type a=$a b=$b c=$c

tell boxsize

echo "crystal type=$type a=$a b=$b c=$c" > pbc.inc

tell bestfft

echo "fftx=$fftx" >> pbc.inc

echo "ffty=$ffty" >> pbc.inc

echo "fftz=$fftz" >> pbc.inc

#remove residues outside the box

removeresidueoutsidebox ext=4 select="all"

#remove residues overlapped

resolveresidueoverlap cutoff=2.2 select="name OH2"

#resolveresidueoverlap cutoff=1.0 select="all"

#check bad overlap

tell contactsamong cutoff=1.5 select="name O*"

#checkmsf

checkmsf

tell msf_info

tell density

echo -hs "| "

echo -hs "|  Summary of solvent box:"

echo -hs "|    box type: $boxtype"

echo -hs "|    size in angstrom: $a x $b x $c"

echo -hs "|    number of residue: $nres"

echo -hs "|    number of atoms: $natom"

echo -hs "|    density: $density"

echo -hs "|    dimmension of FFT suggested: $fftx x $ffty x $fftz"

#resort sequence

atom resortseq  start=1 select=all

tell center select=all

tell size   select=all

#image groups

imggroup method=resid sorted=true select="all"

#nonbond setup

nonbond type=pme nblcutoff=10.0 nbcutoff=8.0 swcutoff=7.0 eps=1.0 \

        beta=0.34 ftx=$fftx fty=$ffty ftz=$fftz bsorder=6

#do minimization for solvent

echo -hs "|  running $nstepmini steps minimization for the solvent box, please wait a moment"

minimize type=SDfuse nstep=$nstepmini nprint=10 ftol=1e-5

minimize type=SD     nstep=$nstepmini nprint=10 ftol=1e-5

tell pot

echo -hs "| total potential energy: $pot kcal/mol"

#save msf and pdb

savemsf file="step7_waterbox.msf"

savepdb fmt=pdb file="step7_waterbox.pdb"