Re: [AMBER] error in rst file during Minimization

From: Stephan Schott <schottve.hhu.de>
Date: Mon, 28 May 2018 15:03:57 +0200

Hi Subrata,
With Amber 16 a change in the default format for coordinate files was set
to netcdf (the binary format you are describing), since is much more
efficient than normal ASCII files. If you would like to have the old
format, please check the ntxo flag in the manual. You can always use
cpptraj or ambpdb to transform these files into something human-readable,
if that is what you need.
Hope it helps,

2018-05-28 14:37 GMT+02:00 Subrata Paul <paul.subrata34.gmail.com>:

> Respected Sir
>
> Very recently, I have installed Amber16 with AmberTools16. I want to
> minimize DNA water system. Therefore I have run this command Line
>
> /home/user/Amber16/amber16/bin/sander -O -i test_min1.in -o
> test_min1.out -p DNA_W.top -c DNA_W.crd -r test_min1.rst -ref
> DNA_W.crd
>
> My out put of the minimization is fine. But, the test_min1.rst looks
> odd, insted of writting the last coordinates it is writting different
> like
> u.<96>@;<9f>ëIþ·ä@2É!µ^D^W<@0?ìªãÍL@<^?^S<8d>¿!^ .
>
> I have attaed the rst file here with
>
> Why this is happening ?
> is there any installation error ?
>
> Any help is appreciable.
>
>
>
> --
>
>
>
>
> *With Best RegardsDr. Subrata PaulUGC-Dr. D. S. Kothari Post Doctoral
> FellowDepartment of Chemical Sciences*
>
> *Tezpur University*
>



-- 
Stephan Schott Verdugo
Biochemist
Heinrich-Heine-Universitaet Duesseldorf
Institut fuer Pharm. und Med. Chemie
Universitaetsstr. 1
40225 Duesseldorf
Germany
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Received on Mon May 28 2018 - 06:30:03 PDT
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