[gmx-users] Dificulties compiling Gromacs 4.0.2 with MOPAC7 QM/MM

Laercio Pol Fachin laercio_pf at yahoo.com.br
Tue Dec 9 16:06:26 CET 2008

That is the right translation for the Portuguese... :)

Well, I removed that line, and "make" gone further, but I stopped in other error:

make[3]: Entrando no diretório `/usr/local/gromacs-4.0.2/src/kernel'
/bin/sh ../../libtool --tag=CC   --mode=link mpicc  -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops   -o grompp grompp.o libgmxpreprocess_mpi.la ../mdlib/libmd_mpi.la ../gmxlib/libgmx_mpi.la  -lxml2  -lnsl -lfftw3f -lm   -lSM -lICE -lX11
mpicc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -o grompp grompp.o  ./.libs/libgmxpreprocess_mpi.a ../mdlib/.libs/libmd_mpi.a ../gmxlib/.libs/libgmx_mpi.a /usr/lib/libxml2.so -lz -lnsl -lfftw3f -lm /usr/lib/libSM.so /usr/lib/libICE.so /usr/lib/libX11.so /usr/lib/libxcb-xlib.so /usr/lib/libxcb.so /usr/lib/libXau.so /usr/lib/libXdmcp.so -ldl
../mdlib/.libs/libmd_mpi.a(qm_mopac.o): In function `call_mopac_SH':
qm_mopac.c:(.text+0x286): undefined reference to `domop_'
../mdlib/.libs/libmd_mpi.a(qm_mopac.o): In function `call_mopac':
qm_mopac.c:(.text+0x83a): undefined reference to `domop_'
../mdlib/.libs/libmd_mpi.a(qm_mopac.o): In function `init_mopac':
qm_mopac.c:(.text+0xc03): undefined reference to `domldt_'
collect2: ld returned 1 exit status
make[3]: ** [grompp] Erro 1
make[3]: Saindo do diretório `/usr/local/gromacs-4.0.2/src/kernel'
make[2]: ** [all-recursive] Erro 1
make[2]: Saindo do diretório `/usr/local/gromacs-4.0.2/src'
make[1]: ** [all] Erro 2
make[1]: Saindo do diretório `/usr/local/gromacs-4.0.2/src'
make: ** [all-recursive] Erro 1

Is there something I should do (better, I forgot to do)?

Thanks in advance,

Message: 2
Date: Tue, 09 Dec 2008 12:26:57 +1100
From: Mark Abraham <Mark.Abraham at anu.edu.au>
Subject: Re: [gmx-users] Dificulties compiling Gromacs 4.0.2 with
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <493DC961.4000808 at anu.edu.au>
Content-Type: text/plain; charset=UTF-8; format=flowed

Laercio Pol Fachin wrote:
> Dear GMX users:
> I'm facing problems installing Gromacs 4.0.2 with mopac7 QM/MM.
> I have downloaded MOPAC7 for SourceForge, as linked in previous mails, 
> and installed it. After, MPICH and fftw 3.0.1. So: "./configure 
> --enable-mpi --with-qmmm-mopac" runs O.K., but, during
> (some shell indications in Portuguese):
> ---
> make[3]: Entrando no diretório `/usr/local/gromacs-4.0.2/src/mdlib'
> /bin/sh ../../libtool --tag=CC   --mode=compile mpicc -DHAVE_CONFIG_H 
> -I. -I../../src -I/usr/include/libxml2 -I../../include 
> -DGMXLIBDIR=\"/usr/local/gromacs/share/top\"   -O3
> -finline-functions -Wall-Wno-unused -funroll-all-loops -MT qm_mopac.lo 
> -MD -MP -MF .deps/qm_mopac.Tpo -c -o qm_mopac.lo qm_mopac.c
>  mpicc -DHAVE_CONFIG_H -I. -I../../src -I/usr/include/libxml2 
> -I../../include
-DGMXLIBDIR=\"/usr/local/gromacs/share/top\" -O3 
> -fomit-frame-pointer -finline-functions -Wall -Wno-unused 
> -funroll-all-loops -MT qm_mopac.lo -MD -MP -MF .deps/qm_mopac.Tpo -c 
> qm_mopac.c -o qm_mopac.o
> qm_mopac.c:52:17: error: nsb.h: Arquivo ou diretório não encontrado

My Portuguese is not so hot, but I figure this error translates as 
"nsb.h: File or directory not found". That means what it says.
version 3.3.x had this file, version 4.x doesn't. I had a look at 
qm_mopac.c and I don't think it was using any of the contents of nsb.h, 
so you should be safe to remove this line from qm_mopac.c. Do let us 
know how you get on.


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