conda activate AmberTools23
mkdir MSI_018
cd MSI_018
xleap
source leaprc.ga
edit PEN
Draw Pentane
Add H and Build in Unit
Close in Unit
savepdb PEN pentane1.pdb
quit
antechamber -i pentane1.pdb - pdb -o pentane1.mol2 -fo mol2
rm A*
xleap
source leaprc.ga
PEN=loadmol2 pentane1.mol2
edit PEN
Select the structure
Relax in Edit
Close in Unit
savepdb PEN pentane2.pdb
quit
antechamber -i pentane2.pdb - pdb -o pentane2.mol2 -fo mol2 -c bcc
rm A* sqm*
xleap
source leaprc.ga
PEN=loadmol2 pentane2.mol2
edit PEN
Check Unit in File
Calculate Net Charge in Unit
Edit Selected Atoms in Edit (make residual charge 0)
Close in Unit
saveo PEN pentane.lib
quit
xleap
source leaprc.water.tip3p
savepdb TP3 tp3.pdb
ff
ff
ff
ff
fi
fi
quit
vi script.packmol
tolerance 2.0
letype pdb
output mixture.pdb
structure pentane2.pdb
number 100
inside box 0.0 0.0 0.0 30.0 30.0 30.0
end structure
structure tp3.pdb
number 500
inside box 0.0 0.0 0.0 30.0 30.0 30.0
end structure
Press esc
:wq
packmol < script.packmol
xleap
source leaprc.ga
loado pentane.lib
source leaprc.water.tip3p
x=loadpdb mixture.pdb
setbox x vdw 0.1
saveamberparm x mixture.prmtop mixture.inpcrd
quit
amb2gro_top_gro.py -p mixture.prmtop -c mixture.inpcrd -t mixture.top -g
mixture.gro -b mixture1.pdb
gmx grompp -f em.mdp -c mixture.gro -p mixture.top -o em.tpr -maxwarn 1
gmx mdrun -v -s em.tpr -o em.trr -c em.gro -e em.edr -g em.log
gmx grompp -f eqm.mdp -c em.gro -p mixture.top -o eqm.tpr -maxwarn 2
gmx mdrun -v -s eqm.tpr -x eqm.xtc -c eqm.gro -e eqm.edr -g eqm.log
gmx grompp -f prd.mdp -c eqm.gro -p mixture.top -o prd.tpr -maxwarn 2
fi
ff
ff
gmx mdrun -v -s prd.tpr -x prd.xtc -c prd.gro -e prd.edr -g prd.log
