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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> >>>> http://lists.ambermd.org/mailman/listinfo/amber
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> >>> AMBER mailing list
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> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
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- application/octet-stream attachment: retk.rst7
- application/octet-stream attachment: min.mdin
Received on Thu Jun 02 2016 - 04:30:02 PDT
