Re: [AMBER] Request .nc to MMPBSA.py?

From: Elvis Martis <elvis_bcp.elvismartis.in>
Date: Mon, 24 Aug 2020 23:48:20 +0530

­čśé ­čĹŹ
Best Regards
Elvis



On Mon, 24 Aug 2020 at 23:47, Camila Mara Clemente <
camilamaraclemente.gmail.com> wrote:

> You are the best!!!!!!!!!!!!!!
>
> It is working!!!!
>
> Thank you!!!!!!!!!
>
> Enviado desde mi iPhone
>
> > El 24 ago. 2020, a la(s) 15:06, Elvis Martis <elvis_bcp.elvismartis.in>
> escribi├│:
> >
> > ´╗┐The command looks ok to me
> > However, there is a problem in the mmpbsa.in. Look at this one I edited
> for
> > you.
> >
> > &general
> > interval=1, netcdf=1,
> > keep_files=0,
> > /
> > &gb
> > igb=8,
> > saltcon=0.0, surften=0.0072,
> > surfoff=0.0, molsurf=0,
> > /
> > &nmode
> > drms=0.001, maxcyc=10000,
> > nminterval=5000, nmendframe=10000,
> > nmode_igb=1,
> > /
> >
> > Best Regards
> > Elvis
> >
> >
> >
> >> On Mon, 24 Aug 2020 at 23:27, Camila Clemente <
> camilamaraclemente.gmail.com>
> >> wrote:
> >>
> >> Hi Elvis!
> >>
> >> When I put:
> >> $AMBERHOME/bin/MMPBSA.py -O -i mmgbsa.in -o
> r_500_prod1.mmgbsa.results.dat
> >> -eo r_500_prod1.mmgbsa.per-frame.dat \
> >> -sp r_500.wet.complex.prmtop -cp r_500.gas.complex.prmtop -rp
> >> r_500.gas.receptor.prmtop -lp r_500_aux.gas.ligand.prmtop -y
> >> r_500_prod1.nc
> >>
> >> I have a error-log:
> >> InputError: Invalid input. Terminate each namelist prior to starting
> >> another one.
> >> Enter `MMPBSA.py --help` for help
> >>
> >> the mmgbsa.in is:
> >> mmgbsa r_500 analysis
> >> &general
> >> interval=1, netcdf=1,
> >> keep_files=0,
> >>
> >> &gb
> >> igb=8,
> >> saltcon=0.0, surften=0.0072,
> >> surfoff=0.0, molsurf=0,
> >>
> >> &nmode
> >> drms=0.001, maxcyc=10000,
> >> nminterval=5000, nmendframe=10000,
> >> nmode_igb=1,
> >> /
> >>
> >> Do you now the mistake?
> >>
> >> When I try with the tutorial amber with .mdcrd i do not have problem
> >>
> >>
> >> El lun., 24 ago. 2020 a las 14:50, Elvis Martis (<
> elvis_bcp.elvismartis.in
> >>> )
> >> escribi├│:
> >>
> >>> Yes!
> >>> That is a valid format.
> >>> Best Regards
> >>> Elvis
> >>>
> >>>
> >>>
> >>> On Mon, 24 Aug 2020 at 23:11, Camila Mara Clemente <
> >>> camilamaraclemente.gmail.com> wrote:
> >>>
> >>>> Hi
> >>>>
> >>>> Can I use my trajectories in format .nc in MMPBSA.py?
> >>>>
> >>>> Thank you
> >>>>
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
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> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>
> >>
> >> --
> >> *Camila*
> >> _______________________________________________
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> >>
> > _______________________________________________
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>
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Received on Mon Aug 24 2020 - 11:30:03 PDT
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