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

From: Elvis Martis <elvis_bcp.elvismartis.in>
Date: Wed, 26 Aug 2020 08:33:44 +0530

Hi Camila
I would set the saltcon to 0.5M while calculating the free energies as well!

On Tuesday, August 25, 2020, Camila Clemente <camilamaraclemente.gmail.com>
wrote:

> Hi Elvis!
>
> I have a question about MMPBSA.py
>
> The complex that I am calculating with MMPBSA.py was simulated with a 0.5M
> NaCl environment. When preparing .mdin for MMPBSA.py I don't know if I
> should set it saltcon= 0.5 or if I should set it to 0.0 because I have
> already simulated it in that environment.
>
> Sorry for asking so many questions!
>
>
>
>
>
> El lun., 24 ago. 2020 a las 15:18, Elvis Martis (<elvis_bcp.elvismartis.in
> >)
> escribi├│:
>
> > ­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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> > > >>>
> > > >>
> > > >>
> > > >> --
> > > >> *Camila*
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>
>
> --
> *Camila*
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-- 
Best Regards
Elvis
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Received on Tue Aug 25 2020 - 20:30:02 PDT
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