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

Laercio Pol Fachin laercio_pf at yahoo.com.br
Thu Dec 11 16:54:59 CET 2008


The LDFLAGS and LIBS I have set manually:

LDFLAGS = /usr/local/mopac7-1.10/src/libmopac.a
LIBS = -lxml2  -lnsl -lfftw3f -lmopac -lm   -lSM -lICE -lX11

Probably, I might have confused the correct "gmxmop.f" and "dcart.f" place: should them stay in the MOPAC folder with files and objects (mopac7-1.10/src) or in LINUX folder with library files (usr/local/lib/)?

Message: 2
Date: Thu, 11 Dec 2008 14:51:34 +0100
From: Gerrit Groenhof <ggroenh at gwdg.de>
Subject: [gmx-users] Re: Dificulties compiling Gromacs 4.0.2 with
	MOPAC7 QM/MM, (Laercio Pol Fachin)
To: gmx-users at gromacs.org
Message-ID: <49411AE6.6020906 at gwdg.de>
Content-Type: text/plain; charset=windows-1252; format=flowed

> Today's Topics:
> Well, I removed that line, and "make" gone further, but I
stopped in other error:
> ---
> make[3]: Entrando no diretório
> /bin/sh ../../libtool --tag=CC   --mode=link mpicc  -O3
-fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loopsÂ
  -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)?
Did you use the gromacs adapted mopac sources? If not, please retreive 
them from the website (below).

Alternatively, you seem to have forgotten to set the LIBS to -lmopac and 
LDFLAGS to the location of the mopac library.


> Thanks in advance,
> Laércio
> 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
> "make":
>> (some shell indications in Portuguese):
>> ---
>> make[3]: Entrando no diretório
>> /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
> -fomit-frame-pointer 
>> -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
> 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
> so you should be safe to remove this line from qm_mopac.c. Do let us 
> know how you get on.
> Mark

      Veja quais são os assuntos do momento no Yahoo! +Buscados
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