The hashed ones are NOT to be loaded in leap.
On Saturday, July 13, 2019, shivangi agarwal <shiviagarwalpharma.gmail.com>
wrote:
> 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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--
Best Regards
Elvis Martis
Mumbai.
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Received on Fri Jul 12 2019 - 21:30:02 PDT
