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
> >)
> escribió:
>
> > 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*
> _______________________________________________
> 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
Received on Mon Aug 24 2020 - 11:30:02 PDT
