Thank you, I didn't know that the default ntxo had changed!
Elisa
On Thu, Jun 2, 2016 at 3:16 PM, David A Case <david.case.rutgers.edu> wrote:
> On Thu, Jun 02, 2016, Elisa Pieri wrote:
> >
> > I'm doing a minimization on a small system (2 residues + a modified one)
> > using a modified parameters file. I'm able to produce the parm7 and rst7
> > using tleap with no problem or error messages, the files are readable
> and I
> > can correctly visualize them using VMD.
> >
> > I used sander (Amber16) with this minimization input:
> >
> > The minimization ended after 40500 steps, but the retk.min.rst7 file is
> > unreadable and VMD cannot open it. Do you know what is it going on?
>
> The default format for restart files has changed in Amber16: it used to be
> a formatted (ascii) file (ntxo=1), but now the default is a netcdf file
> (ntxo=2). This is generally much better for continuing (numbers cannot
> "overflow"), but may not be supported in VMD.
>
> There are a couple of options:
>
> 1. use ambpdb to convert your netcdf restart file to PDB format, and load
> that into VMD.
>
> 2. use cpptraj to convert the netcdf restart to a formatted restart:
>
> cpptraj <<EOF
> parm <your-prmtop-file>
> trajin <your-netcdf-restart-file>
> trajout <choose-a-filename>.rst7 restart
> go
> EOF
>
> (You can also set ntxo=1 for future runs, but the default of ntxo=2 is
> much better for most purposes.)
>
> ....good luck....dac
>
>
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Received on Thu Jun 02 2016 - 06:30:05 PDT
