# merge solute, ions, solvent together

# author: mengen

#

# usage: ./modar step4_merge_all.inp

#

#load force field

include "loadff.inc"

#load solute with contour ions

loadmsf file="step3_with_ions.msf"

#load water box by appending

loadmsf file="step2_solvbox.msf" append=true

#load PBC crystal setup

include "pbc.inc"

#remove overlaping waters

defcls name=solute select="heavyatom && ! resn TIP*"

delete atom select=".byres. ( around solute cut 2.8 && type O* )"

#resort sequence

atom resortseq  start=1 select="resn tip*"

#tell center select=all

#tell size   select=all

tell msf_info

echo -hs "| "

echo -hs "|  Summary of MD system:"

echo -hs "|    number of segments:    $nseg"

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

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

echo -hs "|    number of bonds:       $nbond"

echo -hs "|    number of angles:      $nangl"

echo -hs "|    number of dihedrals:   $ndihe"

echo -hs "|    number of impropers:   $nimpr"

echo -hs "|    number of cross terms: $ncmap"

echo -hs "|    net charge:  $netcharge"

echo -hs "|    total mass:  $totmass"

tell boxsize

echo -hs "|    PBC box: $boxtype, $boxa x $boxb x $boxc"

echo -hs "| "

#checkmsf

checkmsf

#remove fixes if have

atom fix select="none"

savemsf file="step4_all.msf"

savepdb fmt=pdb file="step4_all.pdb"

echo -hs "|  output files:"

echo -hs "|    step4_all.msf"

echo -hs "|    step4_all.pdb"

echo -hs "| "

echo -hs "|  it's time to check the whole MD system by Movar or VMD"

echo -hs "|  it's ready to go next step to do minimization: "

echo -hs "|    ./modar -nobak step5_do_minimization.inp"

echo -hs "| "