Got it. Thank you.
On Sat, Feb 1, 2020 at 9:16 PM Elvis Martis <elvis_bcp.elvismartis.in>
wrote:
> Sorry for the typo
> PBradii=mbondi3
> Best Regards
>
>
>
> On Sun, 2 Feb 2020 at 09:45, Elvis Martis <elvis_bcp.elvismartis.in>
> wrote:
>
> > Yes, it is.
> > Alternatively, you can also set this parameter in leap using
> > PBraii=mbondi3 and not worry about setting it at later stage
> > Best Regards
> >
> >
> >
> > On Sun, 2 Feb 2020 at 08:34, Rui Chen <rchen6.ualberta.ca> wrote:
> >
> >> Dear Elvis,
> >>
> >> Thank you for your answer. It seems like it's necessary to set this
> >> parameter.
> >>
> >> Best regards,
> >> Rui
> >>
> >> On Sat, Feb 1, 2020 at 7:57 PM Elvis Martis <elvis_bcp.elvismartis.in>
> >> wrote:
> >>
> >> > radii=mbondi3 sets the PBradii according to mbondi3. Its mandatory to
> >> > define PBradii for mmpbsa and mmgbsa calculations.
> >> >
> >> > On Sunday, February 2, 2020, Rui Chen <rchen6.ualberta.ca> wrote:
> >> >
> >> > > Hello,
> >> > >
> >> > > I am using ante-MMPBSA.sh to prepare the input files for MMGBSA/PBSA
> >> > > calculations using the following command:
> >> > > ante-MMPBSA.py -p complex_6059_2_20.prmtop -c com.top -r rec.top -l
> >> > lig.top
> >> > > -s ':Na+,Cl-,WAT' -n ':433' --radii=mbondi3
> >> > >
> >> > > What's the purpose of setting radii=mbondi3? I tried to run the
> >> > calculation
> >> > > without "radii=mbondi3" and I got error.
> >> > >
> >> > > Best regards,
> >> > > Rui
> >> > > _______________________________________________
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> >> > >
> >> >
> >> >
> >> > --
> >> > Best Regards
> >> > Elvis Martis
> >> > Mumbai.
> >> > _______________________________________________
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> >> >
> >> _______________________________________________
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> >>
> >
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Received on Sat Feb 01 2020 - 20:30:03 PST
