Re: [AMBER] Problems modifing box lengths in a .rst file.

From: Lucas Bandeira <>
Date: Tue, 18 Dec 2018 13:29:31 -0200

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


On Tue, Dec 18, 2018 at 11:19 AM David A Case <>

> 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 Tue Dec 18 2018 - 08:00:02 PST
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