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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Thu Jun 02 2016 - 02:30:03 PDT
