Re: [AMBER] Installation error

From: Dhananjay <>
Date: Mon, 4 Nov 2013 21:24:46 +0800

Dear all,

I tried clean installation once again, by taking all the suggestions into
account that have been given before.
As previously experienced, I got following error:

use netcdf, only : nf90_double, nf90_float
Fatal Error: Wrong module version '0' (expected '9') for file 'netcdf.mod'
opened at (1)

Further, as per Jeson's suggestion "Try deleting the netcdf.mod file and
then recompiling",
I did "rm include/netcdf.mod "

However, I got following error:

gfortran -DBINTRAJ -c -O3 -mtune=native -ffree-form
-I../../AmberTools/src/pbsa -I../../AmberTools/src/sqm
-I../../AmberTools/src/rism -I../../include -I/opt/amber12/include
-I/opt/amber12/include -o ncsu-umbrella.o ncsu-umbrella.F90

use netcdf, only : nf90_double, nf90_float
Fatal Error: Can't open module file 'netcdf.mod' for reading at (1): No
such file or directory

I just gave a try as follows:

*cp /opt/amber12/AmberTools/include/netcdf.mod /opt/amber12/include/*

This made my installation complete:
Installation of Amber12 (serial) is complete at Mon Nov 4 07:05:07 EST

make[1]: Leaving directory `/opt/amber12/src'

Finally, I ran "make test" which seem successful:

Finished serial test suite for Amber 12 at Mon Nov 4 08:16:21 EST 2013.

make[2]: Leaving directory `/opt/amber12/test'
529 file comparisons passed
9 file comparisons failed
0 tests experienced errors
Test log file saved as
Test diffs file saved as
make[1]: Leaving directory `/opt/amber12/test'

Summary of AmberTools serial tests:

555 file comparisons passed
0 file comparisons failed
1 tests experienced errors
Test log file saved as
No test diffs to save!

I am not sure whether there is problem with my installation OR a common
issue with Debian 7.

Thank you for the suggestions and instructions !!!

-- Joshi

On Fri, Nov 1, 2013 at 8:11 PM, David A Case <>wrote:

> On Fri, Nov 01, 2013, Dhananjay wrote:
> > "./configure gnu" followed by "make install", I am now getting another
> > error as follows:
> >
> > fftw3.F90:10: Error: Can't open included file 'fftw3.f03'
> Things are quite weird here. I'd suggest untarring your
> AmberTools13.tar.bz2
> file to a fresh directory and starting fresh. Something odd seems to be
> going
> on that we can't understand.
> ...dac
> _______________________________________________
> AMBER mailing list

Dhananjay  Joshi
TIGP Graduate Student
Institute of Biological Chemistry
Academia Sinica, Taipei-115, Taiwan
AMBER mailing list
Received on Mon Nov 04 2013 - 05:30:02 PST
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