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 # #
