Hi,
Is trajectory.mdcrd the trajectory file from the QM/MM simulation? Double
check that box info is there with ‘ncdump -h’ and look for the variable
cell_lengths. If it isn’t there then for some reason box info wasn’t
written to the trajectory file. If it is there, cpptraj is missing the info
somehow.
-Dan
On Fri, May 22, 2020 at 4:23 AM emanuele falbo <falbo.emanuele.gmail.com>
wrote:
> 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 ?
>
> Cheers,
> Manuele
>
>
>
>
>
> Il giorno gio 21 mag 2020 alle ore 19:05 David A Case <
> david.case.rutgers.edu> 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 trajectory.nc 200 200 1
> > >trajout restart_200th.rst7 restart
> > >run
> > >
> >
> > ....dac
> >
> >
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> >
>
>
> --
>
> *Emanuele Falbo*
> PhD student
> Penfold group
> School of Natural and Environmental Sciences
> Bedson Building, Newcastle University
> Newcastle upon Tyne, NE1 7RU
> w: http://tompenfoldresearch.weebly.com/
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>
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Received on Fri May 22 2020 - 05:00:01 PDT
