Hi,
FYI you can convert the netcdf restart to the old ASCII format (for
e.g. vmd on windows) using cpptraj:
cpptraj -p <topology file> -y <netdf restart> -x myfile.rst7
Hope this helps,
-Dan
On Sun, Jun 21, 2020 at 9:05 AM Houcemeddine Othman <houcemoo.gmail.com> wrote:
>
> Thank for the reply,
> I did not know that as I used to work with version 12 of Amber. It is
> indeed a netcdf file.
> The reason why I said they are incompatible, is that I failed to load the
> files in vmd and ambpdb and I though that by specifying the extension will
> be sufficient to write an rst file.
>
> Regards
>
>
> On Sun, Jun 21, 2020 at 3:22 AM David A Case <david.case.rutgers.edu> wrote:
>
> > On Sat, Jun 20, 2020, Houcemeddine Othman wrote:
> >
> > >I am running a restrained minimization step of a
> > >protein+solvent+counterions system using the following input
> > >
> > >minimization parameters
> > >&cntrl
> > >imin = 1, maxcyc = 7000, ncyc = 1000, cut = 12, ntb = 1, ntr = 0, igb = 0,
> > >drms = 0.01
> > >/
> > >sander -O -i energy_min1.in -o energy_min1.out -c sructure_start.rst7 -p
> > >structure.prmtop -r structure_min1.rst7 -ref sructure_start.rst7
> > >
> > >Everything runs successfully. However, the resulting minimized structure
> > >(structure_min1.rst7) contains lesser information (2 Mb) than the starting
> > >structure (sructure_start.rst7, 3Mb). It is also not compatible with the
> > >topology file (structure.prmtop).
> >
> > The default format for restart files is netcdf, which will often by
> > smaller than a formatted form. Use the "file" command to see which
> > files are formatted ("ASCII") and which are not ("data").
> >
> > [The ntxo variable controls the format of restart files; but we
> > recommend sticking with the default unless you know you have a good
> > reason not to.]
> >
> > How did you conclude that the min1 restart file is not compatible with
> > the prmtop file?
> >
> > ....dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> Houcemeddine Othman
> www.bioinfo-on-dunes.net
> Sydney Brenner Institute of molecular bioscience
> University of the Witwatersrand
> The Mount, 9 Jubilee Road,
> Parktown 2193, Johannesburg,
> Gauteng, South Africa.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 24 2020 - 05:30:07 PDT
