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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> > > AMBER.ambermd.org
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> > >
> >
> >
> > --
> > Best Regards
> > Elvis Martis
> > Mumbai.
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Sat Feb 01 2020 - 20:30:02 PST
