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