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

From: Camila Clemente <camilamaraclemente.gmail.com>
Date: Tue, 25 Aug 2020 15:28:17 -0300

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
> > >>>>
> > >>> _______________________________________________
> > >>> AMBER mailing list
> > >>> AMBER.ambermd.org
> > >>> http://lists.ambermd.org/mailman/listinfo/amber
> > >>>
> > >>
> > >>
> > >> --
> > >> *Camila*
> > >> _______________________________________________
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> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >>
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> >
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> >
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-- 
*Camila*
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Received on Tue Aug 25 2020 - 11:30:02 PDT
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