Hi Elisa,
VMD cannot yet read the NetCDF restart file format (there is most likely
nothing wrong with the file). If you need to read this file into VMD, you
will need to convert it to a format VMD reads first (e.g., using cpptraj).
Something like:
cpptraj -p retk.parm7 -y retk.rst7 -x retk_ascii.rst7
HTH,
Jason
On Thu, Jun 2, 2016 at 7:02 AM, Elisa Pieri <elisa.pieri90.gmail.com> wrote:
> Hi Bill,
>
> I tried both with no results, nothing changed. I'm attaching my parm7,
> initial rst7 and mdin files, maybe it helps you.
>
> Elisa
>
> On Thu, Jun 2, 2016 at 12:50 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
> > Another interesting thing to try would be to see if you can start md
> > from that rst.
> >
> > Bill
> >
> >
> > On 6/2/16 3:20 AM, Bill Ross wrote:
> > > Hi Elisa,
> > >
> > > So it seems to be NetCDF due to the initial CDF. Perhaps it got
> > > corrupted due to bug or external factor. I would run a short
> > > minimization and see how that does for visibility, and compare file
> > sizes.
> > >
> > > Bill
> > >
> > >
> > > On 6/2/16 2:23 AM, Elisa Pieri wrote:
> > >> Hi Bill,
> > >>
> > >> thank you for your fast reply.
> > >>
> > >> If I open the rst7 with VIM, I see this:
> > >> CDF^B^.^.^.^.^.^.^.
> > >>
> >
> ^.^.^.^B^.^.^.^Gspatial^.^.^.^.^C^.^.^.^Datom^.^.^.a^.^.^.^L^.^.^.^F^.^.^.^Etitle^.^.^.^.^.^.^B^.^.^.^Ldefault_name^.^.^.^Kapplication^.^.^.^.^B^.^.^.^EAMBER^.^.^.^.^.^.^Gprogram^.^.^.^.^B^.^.^.^Fsander^.^.^.^.^.^NprogramVersion^.^.^.^.^.^B^.^.^.^D16.0^.^.^.^KConventions^.^.^.^.^B^.^.^.^LAMBERRESTART^.^.^.^QConventionVersion^.^.^.^.^.^.^B^.^.^.^C1.0^.^.^.^.^K^.^.^.^C^.^.^.^Dtime^.^.^.^.^.^.^.^L^.^.^.^A^.^.^.^Eunits^.^.^.^.^.^.^B^.^.^.
> > >>
> > >> I used this command to open it in VMD (as I usually do):
> > >>
> > >> vmd -parm7 retk.parm7 -rst7 retk.min.rst7
> > >>
> > >> and also loading -rst7 retk.min.rst7 as NetCDF, but still no results.
> > >>
> > >> Elisa
> > >>
> > >>
> > >>
> > >>
> > >> On Thu, Jun 2, 2016 at 11:17 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> > >>
> > >>> What does 'file retk.min.rst7' tell you? What file type did you tell
> > >>> VMD? There are a few to try I think.
> > >>>
> > >>> Bill
> > >>>
> > >>>
> > >>> On 6/2/16 1:51 AM, Elisa Pieri wrote:
> > >>>> Hello,
> > >>>>
> > >>>> 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:
> > >>>>
> > >>>> &cntrl
> > >>>> imin = 1,
> > >>>> maxcyc = 50000,
> > >>>> ncyc = 500,
> > >>>> ntb = 0,
> > >>>> igb = 0,
> > >>>> cut = 1000,
> > >>>> ntxo = 2
> > >>>> /
> > >>>>
> > >>>> and this command:
> > >>>>
> > >>>> sander -O -i min.mdin -p retk.parm7 -c retk.rst7 -ref retk.rst7 -o
> > >>>> retk.min.mdout -r retk.min.rst7
> > >>>>
> > >>>> 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?
> > >>>>
> > >>>> Thank you for your help,
> > >>>>
> > >>>> Elisa
> > >>>> _______________________________________________
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Jason M. Swails
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Received on Thu Jun 02 2016 - 06:30:04 PDT
