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 - 20:30:02 PST
