OK. Thank you very much. You helped me a lot.
A managed to solve the problem. I have done another NPT simulation but I
generated a ".rst7" file instead of a ".rst" file. Then I did what Daniel
said to me previously, I used cpptraj to generate a restart file with the
box lengths in it.
When I tried to use the latter restart file in another simulation
everything worked well.
Thank you for all the help.
Lucas Bandeira
On Tue, Dec 18, 2018 at 3:45 PM David Cerutti <dscerutti.gmail.com> wrote:
> 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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Received on Wed Dec 19 2018 - 07:30:03 PST
