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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Received on Sat Feb 01 2020 - 19:30:02 PST
