>
> tleap
> source leaprc.gaff
> source leaprc.protein.ff14SB
> loadAmberParams ligand.frcmod
> loadoff atomic_ions.lib
Try leaving this out.
> loadoff ligand.lib
> loadAmberParams frcmod.ions234lm_iod_tip3p
Try leaving this out.
> com=loadpdb complex_42_final_2_noH.pdb
> savepdb com see.pdb
> saveAmberParm com see.prmtop see.inpcrd
> source leaprc.water.tip3p
> solvateBox com TIP3PBOX 10.0
> charge com
> loadoff ions94.lib
Ooh... leave this out...it is 25 years old.
> addions com Na+ 6
> loadamberparams frcmod.ionsjc_tip3p
Leave this out...it has already been loaded..
> saveAmberParm com see.prmtop see.inpcrd
> savepdb com see-box.pdb
>
> saveAmberParm com see-box.inpcrd see-box.prmtop
You should use AmberTools19 if you are not doing so. Just load one leaprc for proteins, and one leaprc for ions
....dac
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Received on Fri Jul 12 2019 - 13:00:02 PDT
