Re: [AMBER] Questions regarding Installation of AMBER 16

From: Daniel Roe <>
Date: Mon, 12 Dec 2016 14:52:07 -0500

On Sun, Dec 11, 2016 at 4:07 PM, James Kress <> wrote:
> Everything went fine except I was given a warning about the absence of
> parallel NetCDF. I searched the AMBER 16 distribution but could find no
> trace of pnetcdf. Do I need to install this separately?

Yes, but as Hai mentioned it's only if you want to write NetCDF
trajectories with cpptraj.MPI. If you do, compilation is relatively
straightforward. You can even install it to AMBERHOME and then specify
that to Amber's configure, e.g.

cd <parallel netcdf source dir>
./configure --prefix=$AMBERHOME
make install
./configure -mpi --with-pnetcdf $AMBERHOME gnu


Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
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Received on Mon Dec 12 2016 - 12:00:03 PST
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