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 - 06:30:04 PDT
