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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Received on Thu Jun 02 2016 - 04:00:02 PDT
