Indeed, ChBox is a 50-line C program that only works with inpcrd files and
formatted restart files. Since cpptraj (and even tleap) have these
capabilities there is no need for ChBox anymore.
Dave
On Tue, Dec 18, 2018 at 12:18 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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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>
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Received on Tue Dec 18 2018 - 10:00:05 PST
