export AMBERHOME=/home/jonathan/amber12/

$AMBERHOME/bin/antechamber -i 2ndOH.pdb -fi pdb -o 2ndOH.mol2 -fo mol2 -s 2

$AMBERHOME/bin/parmchk -i 2ndOH.mol2 -f mol2 -o 2ndOH.frcmod

$AMBERHOME/bin/tleap -f leaprc.ff99SB

source leaprc.gaff

2ndOH = loadmol2 2ndOH.mol2

check 2ndOH

loadamberparams 2ndOH.frcmod

saveoff 2ndOH 2ndOH.lib


solvatebox 2ndOH TIP3PBOX 15

saveamberparm 2ndOH 2ndOH.prmtop 2ndOH.inpcrd