AMBER ff12SB

Make sure that AMBERHOME points to /usr/local/amber12. 

#
# cat leap.script 
source leaprc.ff12SB
loadamberparams frcmod.ionsjc_tip3p
test = loadPdb aligned.pdb
check test
solvateBox test TIP3PBOX 7.0 iso
addions test Na+ 2
saveAmberParm test test.prmtop test.crd
savepdb test test.pdb
#
#
# tleap -s -f leap.script
#
# vmd -dispdev text test.prmtop test.crd
set all [atomselect top all]
$all writepsf ionized.psf
quit
#
#




AMBER ff14SB

Make sure that AMBERHOME points to /usr/local/amber16. 

#
# cat leap.script 
source leaprc.protein.ff14SB
source leaprc.water.tip3p
loadamberparams frcmod.ionsjc_tip3p
aLa = loadPdb aligned.pdb
check aLa
solvateBox aLa TIP3PBOX 8.0 iso
addions aLa Cl- 0
saveAmberParm aLa aLa.prmtop aLa.crd
savepdb aLa aLa.pdb
#
#
# tleap -s -f leap.script
#
# vmd -dispdev text test.prmtop test.crd
set all [atomselect top all]
$all writepsf ionized.psf
quit
#
#