Re: [AMBER] Installation error

From: Jason Swails <>
Date: Thu, 31 Oct 2013 07:22:25 -0400

On Thu, Oct 31, 2013 at 7:07 AM, Dhananjay <>wrote:

> Thank you for the suggestions.
> Unfortunately, I don't have Intel compiles right now, therefore, tried
> installation with gnu.
> The argument I gave to configure is: ./configure gnu
> As per the David's suggestion, I make uninstall and then configured and
> compiled again with the above argument.
> Following is the error message I got:
> Warning: Type mismatch in argument 'c' at (1); passed COMPLEX(8) to REAL(8)
> -DHASBZ2 -I/opt/amber12/include -o cluster.o cluster.c
> -DHASBZ2 -I/opt/amber12/include -o clusterLib.o clusterLib.c
> -DHASBZ2 \
> -o rdparm main.o rdparm.o dispatch.o help.o utility.o second.o io.o
> trajectory.o netcdf_ptraj.o parallel_ptraj.o evec.o torsion.o mask.o rms.o
> display.o interface.o energy.o experimental.o ptraj.o actions.o analyze.o
> thermo.o pubfft.o cluster.o clusterLib.o -L/opt/amber12/lib -lpdb -larpack
> -llapack -lblas -lgfortran -w -L/opt/amber12/lib -lnetcdf -lm
> /usr/bin/ld: cannot find -lnetcdf

Try deleting the netcdf.mod file and then recompiling.

cd /opt/amber12
rm include/netcdf.mod
make install

Does that work?

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Thu Oct 31 2013 - 04:30:03 PDT
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