Re: [AMBER] Error in saving prmtop and inpcrd

From: shivangi agarwal <shiviagarwalpharma.gmail.com>
Date: Sat, 13 Jul 2019 09:47:39 +0530

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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> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> Best Regards
> Elvis Martis
> Mumbai.
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Received on Fri Jul 12 2019 - 21:30:02 PDT
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