Re: [AMBER] error in rst file during Minimization

From: Subrata Paul <paul.subrata34.gmail.com>
Date: Mon, 28 May 2018 21:34:38 +0530

thanks stephen


On Mon, May 28, 2018, 6:35 PM Stephan Schott <schottve.hhu.de> wrote:

> 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 - 09:30:02 PDT
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