Re: [AMBER] QM/MM MD: Error reading box

From: emanuele falbo <>
Date: Fri, 22 May 2020 09:23:23 +0100

Hi Daniel,

There are the differences:
there is no box info bottom in the 220th_restart.rst7 file. The number of
lines is actually different
,i.e., 717 (file.rst7) and 4602 ( 220th_restart.rst7), since the first is a
netcdf file, while the second an ascii one.

Just to make it clear, in cpptraj I get :

>parm topology.prmtop
>trajin trajectory.mdcrd 220 220 1
 [trajin trajectory.mdcrd]
        Reading 'trajectory.mdcrd' as Amber NetCDF
Warning: Box information present in topology but not in trajectory.
Warning: DISABLING BOX in topology 'topology.prmtop'!

Could it be that sander didn't print out the box info into the trajectory
during the minimization ?


Il giorno gio 21 mag 2020 alle ore 19:05 David A Case <> ha scritto:

> On Thu, May 21, 2020, emanuele falbo wrote:
> >
> >*Note that if I use the file.rst7 from the minimization, which would
> >correspond to the last frame, the MD goes like a charm. This makes me
> >thing that the box is present,*
> You can just look at the bottom of the restart file to see if the box
> info is on the last line. Also, do other comparisons between the two
> rst7 file: are they the same size, number of lines, etc?
> >
> >*but there is something wrong when extracting the frame in cpptraj. In
> >cpptraj the way I do is:*
> >
> >parm topology.prmtop
> >trajin 200 200 1
> >trajout restart_200th.rst7 restart
> >run
> >
> ....dac
> _______________________________________________
> AMBER mailing list

*Emanuele Falbo*
PhD student
Penfold group
School of Natural and Environmental Sciences
Bedson Building, Newcastle University
Newcastle upon Tyne, NE1 7RU
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Received on Fri May 22 2020 - 01:30:02 PDT
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