If I am correct, the hashed one I have to leave as per your suggestion,
tleap
source leaprc.gaff
source leaprc.protein.ff14SB
loadAmberParams ligand.frcmod
#loadoff atomic_ions.lib
loadoff ligand.lib
#loadAmberParams frcmod.ions234lm_iod_tip3p
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
addions com Na+ 6
#loadamberparams frcmod.ionsjc_tip3p
saveAmberParm com see.prmtop see.inpcrd
savepdb com see-box.pdb
But, when I am leaving out loadoff atomic_ions.lib, I am getting "FATAL:
Atom .R<ZN 260>.A<ZN 1> does not have a type".
and when I am leaving out #loadoff ions94.lib, Error: addIons: Argument #2
is type String must be of type: [unit].
I don't know what to do...
On Sat, Jul 13, 2019 at 1:07 AM David Case <dacase1.gmail.com> wrote:
>
> >
> > 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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>
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Received on Fri Jul 12 2019 - 21:30:02 PDT
