Could you send me your input files (including your coordinate files and the
additional parameters you need to load) off the list?
Best Regards
Elvis Martis
On Sat, 13 Jul 2019 at 09:54, shivangi agarwal <shiviagarwalpharma.gmail.com>
wrote:
> Ya, that is what I am doing but getting other errors as mentioned above
>
> On Sat, Jul 13, 2019 at 9:52 AM Elvis Martis <elvis_bcp.elvismartis.in>
> wrote:
>
> > 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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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Fri Jul 12 2019 - 22:00:02 PDT
