Hi,
Did you follow the advice I sent in my previous mail and make certain
the file you are writing is being written in the correct format? An
ASCII restart will have a title followed by number of atoms and then 6
columns og numbers, e.g.
trajectory generated by ptraj
223
-1.8890000 9.1590000 7.5690000 -1.0370000 8.6910000 7.2960000
...
If it doesn't look like that then you are using the wrong format.
-Dan
On Tue, Dec 18, 2018 at 10:30 AM Lucas Bandeira
<bandeiralucas97.gmail.com> wrote:
>
> Actually the first problem that I had was: when I had tried to run a
> simulation using a normal restart file (.rst) the following message was
> shown in the output file:
>
> | Flags: MPI
> getting box info from netcdf restart file
> | NetCDF restart box info found
> |Largest sphere to fit in unit cell has radius = 0.000
> ASSERTion 'e' failed in ew_setup.F90 at line 306.
>
> When I did what Dan said, use cpptraj to add box lengths in the restart
> file, I got this message:
>
> | Flags: MPI
> getting new box info from bottom of inpcrd
> | INFO: Old style inpcrd file read
>
> ERROR: I could not find the number of atoms or the time on
> the second line of your inpcrd file [New_2NPT.rst]. Bad INPCRD file!
>
> When I specify the restart format (trajout New_2NPT.rst restart) in the
> cpptraj input file I have this message:
>
> | Flags: MPI
> getting new box info from bottom of inpcrd
> | INFO: Old style inpcrd file read
>
> | peek_ewald_inpcrd: Box info not found in inpcrd
>
> I hope I have been clear
>
> Lucas
>
> On Tue, Dec 18, 2018 at 11:19 AM David A Case <david.case.rutgers.edu>
> wrote:
>
> > On Mon, Dec 17, 2018, Lucas Bandeira wrote:
> > >
> > >I'm trying to modify the box lengths in a .rst file according to AMBER
> > >Advance Tutorial Section 2. I want to add the average box length in the
> > >restart file, but I have no idea what to do, I have tried ChBox, but it
> > >doesn't work.
> >
> > "It doesn't work" doesn't give us much information to go on. Can you
> > say what you tried, and what the result was? Is your .rst file a
> > formatted file, or netcdf?
> >
> > Given that cpptraj has this capability (albeit with a more complicated
> > input file), we might need to retire ChBox (which I think only works
> > with formatted restart files.) But I'm hesitant to do that, since there
> > are presumably lots of scripts out there that use this program. So I'd
> > like to know what is wrong.
> >
> > [We could proceed as with ambpdb, mimicking the ChBox command with a
> > cpptraj script.]
> >
> > ...thanks...dac
> >
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Tue Dec 18 2018 - 09:30:03 PST
