On Mon, Jan 25, 2016 at 11:19 AM, Aishani Prem <aishaniprem.gmail.com> wrote:
> Hi,
> I have been trying to run simulations in amber. When I used the
> command --
>
> mpirun -np 8 $AMBERHOME/bin/sander -O -i test_gb_md1_nocut.in -o
This is wrong. You should use sander.MPI for parallel runs, not sander.
> cd $AMBERHOME
> ./configure -mpi gnu
>
> I get an error--
> IOError: [Errno 13] Permission denied:
> '.patches/AmberTools15_Unapplied_Patches/update.4'
There appears to be something wrong with the permissions of the files
in your Amber directory tree. The best solution may be to start from a
clean build (i.e. unpack Amber from the original tarball into a new
directory).
-Dan
>
> Where am I going wrong?
>
>
>
>
> --
> Thank You and Regards,
> Aishani Chittoor Prem
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Mon Jan 25 2016 - 11:30:03 PST
