Please use as follows
source leaprc.water.tip3p
solvateBox com TIP3PBOX 10.0
addions com Na+ 6
saveAmberParm com see-box.inpcrd see-box.prmtop
Best Regards
Elvis Martis
On Fri, 12 Jul 2019 at 14:48, shivangi agarwal <shiviagarwalpharma.gmail.com>
wrote:
> Hi
> I have loaded all the parameters mentioned below, then also it is showing
> error
> source leaprc.water.tip3p
> solvateBox com TIP3PBOX 10.0
> loadoff ions94.lib
> addions com Na+ 6
> loadamberparams frcmod.ionsjc_tip3p
> loadamberparams frcmod.ionsff99_tip3p
> loadamberparams frcmod.ions1lm_iod
> loadamberparams frcmod.ions1lm_1264_tip3p
> loadamberparams frcmod.ions1lm_126_hfe_opc
> loadamberparams frcmod.ions1lm_126_iod_opc
> saveAmberParm com see-box.inpcrd see-box.prmtop
>
> On Fri, Jul 12, 2019 at 2:45 PM Elvis Martis <elvis_bcp.elvismartis.in>
> wrote:
>
> > You forgot load parameters for ions
> > source leaprc.water.tip3p
> > Best Regards
> > Elvis Martis
> >
> >
> > On Fri, 12 Jul 2019 at 14:21, shivangi agarwal <
> > shiviagarwalpharma.gmail.com>
> > wrote:
> >
> > > While saving prmtop and inpcrd, after solvation and addition of
> ions(Na+
> > > 6), I am getting error as
> > >
> > > saveAmberParm com see-box.inpcrd see-box.prmtop
> > > Checking Unit.
> > > Building topology.
> > > Building atom parameters.
> > > Error: For atom (.R<Na+ 9705>.A<Na+ 1>) could not find vdW (or other)
> > > parameters for type (IP)
> > > Error: For atom (.R<Na+ 9706>.A<Na+ 1>) could not find vdW (or other)
> > > parameters for type (IP)
> > > Error: For atom (.R<Na+ 9707>.A<Na+ 1>) could not find vdW (or other)
> > > parameters for type (IP)
> > > Error: For atom (.R<Na+ 9708>.A<Na+ 1>) could not find vdW (or other)
> > > parameters for type (IP)
> > > Error: For atom (.R<Na+ 9709>.A<Na+ 1>) could not find vdW (or other)
> > > parameters for type (IP)
> > > Error: For atom (.R<Na+ 9710>.A<Na+ 1>) could not find vdW (or other)
> > > parameters for type (IP)
> > > Warning: Parameter file was not saved.
> > >
> > > Can anyone suggest?.
> > > _______________________________________________
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> >
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Received on Fri Jul 12 2019 - 03:00:02 PDT
