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
>
>
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>
--
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.
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Received on Sun Jun 21 2020 - 06:30:04 PDT
