<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Hi!<br><br>Now, I tried to configure Mopac QMMM not manually, that is:<br><br>"./configure --enable-mpi --with-qmmm-mopac CPPFLAGS=-DUSE_MOPAC LIBS=-lmopac LDFLAGS=-L/usr/local/mopac7-1.10/src"<br><br>It ran O.K., but I had other problem now:<br><br>---<br><br>ranlib .libs/libgmxpreprocess_mpi.a<br>creating libgmxpreprocess_mpi.la<br>(cd .libs && rm -f libgmxpreprocess_mpi.la && ln -s ../libgmxpreprocess_mpi.la libgmxpreprocess_mpi.la)<br>mpicc -DHAVE_CONFIG_H -I. -I../../src -I/usr/include/libxml2 -I../../include -DGMXLIBDIR=\"/usr/local/gromacs/share/top\" -DUSE_MOPAC -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -MT grompp.o -MD -MP -MF .deps/grompp.Tpo -c -o grompp.o grompp.c<br>mv -f .deps/grompp.Tpo .deps/grompp.Po<br>/bin/sh ../../libtool --tag=CC --mode=link mpicc -O3
-fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -L/usr/local/mopac7-1.10/src -o grompp grompp.o libgmxpreprocess_mpi.la ../mdlib/libmd_mpi.la ../gmxlib/libgmx_mpi.la -lxml2 -lnsl -lfftw3f -lm -lmopac -lSM -lICE -lX11<br>mpicc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -o grompp grompp.o -L/usr/local/mopac7-1.10/src ./.libs/libgmxpreprocess_mpi.a ../mdlib/.libs/libmd_mpi.a ../gmxlib/.libs/libgmx_mpi.a /usr/lib/libxml2.so -lz -lnsl -lfftw3f -lm -lmopac /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<br>/usr/local/mopac7-1.10/src/libmopac.a(lread.o): In function `e_rsle':<br>(.text+0x160): undefined reference to `__ctype_b'<br>/usr/local/mopac7-1.10/src/libmopac.a(lread.o): In function `e_rsle':<br>(.text+0x21f): undefined reference to
`__ctype_b'<br>/usr/local/mopac7-1.10/src/libmopac.a(lread.o): In function `e_rsle':<br>(.text+0x296): undefined reference to `__ctype_b'<br>/usr/local/mopac7-1.10/src/libmopac.a(lread.o): In function `e_rsle':<br>(.text+0x2d0): undefined reference to `__ctype_b'<br>/usr/local/mopac7-1.10/src/libmopac.a(lread.o): In function `e_rsle':<br>(.text+0x8b2): undefined reference to `__ctype_b'<br>/usr/local/mopac7-1.10/src/libmopac.a(lread.o):(.text+0xb05): more undefined references to `__ctype_b' follow<br>collect2: ld returned 1 exit status<br>make[3]: ** [grompp] Erro 1<br>make[3]: Saindo do diretório `/usr/local/gromacs-4.0.2/src/kernel'<br>make[2]: ** [all-recursive] Erro 1<br>make[2]: Saindo do diretório `/usr/local/gromacs-4.0.2/src'<br>make[1]: ** [all] Erro 2<br>make[1]: Saindo do diretório `/usr/local/gromacs-4.0.2/src'<br>make: ** [all-recursive] Erro 1<br><br>---<br><br>I tried it with both Gromacs 4.0.2 and 3.3.3, and the same output error
appears; so, probably, it's something I forgot... Any idea?<br><br>Laércio<br><br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><pre><br>Message: 4<br>Date: Fri, 12 Dec 2008 10:18:20 +0100<br>From: Gerrit Groenhof <ggroenh@gwdg.de><br>Subject: [gmx-users] Re: Dificulties compiling Gromacs 4.0.2 with,<br> MOPAC7 QM/MM<br>To: gmx-users@gromacs.org<br>Message-ID: <49422C5C.2060900@gwdg.de><br>Content-Type: text/plain; charset=windows-1252; format=flowed<br><br>Ok, but somehow these flags do not show up in the compilation output <br>(bit messy copy/paste):<br><br>> mpicc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused<br>> <br>-funroll-all-loops -o grompp grompp.o ./.libs/libgmxpreprocess_mpi.a<br>../mdlib/.libs/libmd_mpi.a ../gmxlib/.libs/libgmx_mpi.a /usr/lib/libxml2.so -lz<br>-lnsl -lfftw3f -lm /usr/lib/libSM.so /usr/lib/libICE.so
/usr/lib/libX11.so<br>/usr/lib/libxcb-xlib.so /usr/lib/libxcb.so /usr/lib/libXau.so<br>/usr/lib/libXdmcp.so -ldl<br><br>There should be a -lmopac somewhere then.<br><br>Try a make distclean, and reconfigure with the LIBS and LDFLAGS set.<br><br>GErrit<br><br>><br>> ------------------------------<br>><br>> Message: 4<br>> Date: Thu, 11 Dec 2008 07:54:59 -0800 (PST)<br>> From: Laercio Pol Fachin <laercio_pf@yahoo.com.br><br>> Subject: [gmx-users] Re: Dificulties compiling Gromacs 4.0.2 with<br>> MOPAC7 QM/MM<br>> To: gmx-users@gromacs.org<br>> Message-ID: <554128.85516.qm@web51510.mail.re2.yahoo.com><br>> Content-Type: text/plain; charset="utf-8"<br>><br>> Well...<br>><br>> The LDFLAGS and LIBS I have set manually:<br>><br>> LDFLAGS = /usr/local/mopac7-1.10/src/libmopac.a<br>> LIBS = -lxml2 -lnsl -lfftw3f -lmopac -lm  -lSM -lICE -lX11<br>><br>> Probably, I might have confused
the correct "gmxmop.f" and<br>"dcart.f" place: should them stay in the MOPAC folder with files and<br>objects (mopac7-1.10/src) or in LINUX folder with library files<br>(usr/local/lib/)?<br>><br>> Laércio<br>> Message: 2<br>> Date: Thu, 11 Dec 2008 14:51:34 +0100<br>> From: Gerrit Groenhof <ggroenh@gwdg.de><br>> Subject: [gmx-users] Re: Dificulties compiling Gromacs 4.0.2 with<br>> MOPAC7 QM/MM, (Laercio Pol Fachin)<br>> To: gmx-users@gromacs.org<br>> Message-ID: <49411AE6.6020906@gwdg.de><br>> Content-Type: text/plain; charset=windows-1252; format=flowed<br>><br>><br>> <br>>> Today's Topics:<br>>><br>>><br>>> Well, I removed that line, and "make" gone further, but I<br>>> <br>> stopped in other error:<br>> <br>>> ---<br>>> make[3]: Entrando no diretório<br>>> <br>> `/usr/local/gromacs-4.0.2/src/kernel'<br>>
<br>>> /bin/sh ../../libtool --tag=CC  --mode=link mpicc -O3<br>>> <br>> -fomit-frame-pointer -finline-functions -Wall -Wno-unused<br>-funroll-all-loopsÂ<br>>  -o grompp grompp.o libgmxpreprocess_mpi.la ../mdlib/libmd_mpi.la<br>> ../gmxlib/libgmx_mpi.la -lxml2 -lnsl -lfftw3f -lm  <br>-lSM -lICE -lX11<br>> <br>>> mpicc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused<br>>> <br>> -funroll-all-loops -o grompp grompp.o ./.libs/libgmxpreprocess_mpi.a<br>> ../mdlib/.libs/libmd_mpi.a ../gmxlib/.libs/libgmx_mpi.a<br>/usr/lib/libxml2.so -lz<br>> -lnsl -lfftw3f -lm /usr/lib/libSM.so /usr/lib/libICE.so /usr/lib/libX11.so<br>> /usr/lib/libxcb-xlib.so /usr/lib/libxcb.so /usr/lib/libXau.so<br>> /usr/lib/libXdmcp.so -ldl<br>> <br>>> ../mdlib/.libs/libmd_mpi.a(qm_mopac.o): In function<br>`call_mopac_SH':<br>>>
qm_mopac.c:(.text+0x286): undefined reference to `domop_'<br>>> ../mdlib/.libs/libmd_mpi.a(qm_mopac.o): In function `call_mopac':<br>>> qm_mopac.c:(.text+0x83a): undefined reference to `domop_'<br>>> ../mdlib/.libs/libmd_mpi.a(qm_mopac.o): In function `init_mopac':<br>>> qm_mopac.c:(.text+0xc03): undefined reference to `domldt_'<br>>> collect2: ld returned 1 exit status<br>>> make[3]: ** [grompp] Erro 1<br>>> make[3]: Saindo do diretório<br>`/usr/local/gromacs-4.0.2/src/kernel'<br>>> make[2]: ** [all-recursive] Erro 1<br>>> make[2]: Saindo do diretório `/usr/local/gromacs-4.0.2/src'<br>>> make[1]: ** [all] Erro 2<br>>> make[1]: Saindo do diretório `/usr/local/gromacs-4.0.2/src'<br>>> make: ** [all-recursive] Erro 1<br>>> ---<br>>><br>>> Is there something I should do (better, I forgot to do)?<br>>> <br>>> <br>> Did you use
the gromacs adapted mopac sources? If not, please retreive <br>> them from the website (below).<br>><br>> Alternatively, you seem to have forgotten to set the LIBS to -lmopac and <br>> LDFLAGS to the location of the mopac library.<br>><br>> Gerrit<br>><br>><br>> <br>>> Thanks in advance,<br>>> Laércio<br>>><br>>><br>>><br>>> Message: 2<br>>> Date: Tue, 09 Dec 2008 12:26:57 +1100<br>>> From: Mark Abraham <Mark.Abraham@anu.edu.au><br>>> Subject: Re: [gmx-users] Dificulties compiling Gromacs 4.0.2 with<br>>> MOPAC7 QM/MM<br>>> To: Discussion list for GROMACS users <gmx-users@gromacs.org><br>>> Message-ID: <493DC961.4000808@anu.edu.au><br>>> Content-Type: text/plain; charset=UTF-8; format=flowed<br>>><br>>> Laercio Pol Fachin wrote:<br>>> <br>>> <br>>>> Dear GMX
users:<br>>>><br>>>> I'm facing problems installing Gromacs 4.0.2 with mopac7<br>QM/MM.<br>>>><br>>>> I have downloaded MOPAC7 for SourceForge, as linked in previous<br>mails,<br>>>> <br>><br>> <br>>>> and installed it. After, MPICH and fftw 3.0.1. So:<br>"./configure <br>>>> --enable-mpi --with-qmmm-mopac" runs O.K., but, during<br>>>> <br>>>> <br>>> "make":<br>>> <br>>> <br>>>> (some shell indications in Portuguese):<br>>>> ---<br>>>> make[3]: Entrando no diretório<br>>>> <br>> `/usr/local/gromacs-4.0.2/src/mdlib'<br>> <br>>>> /bin/sh ../../libtool --tag=CC --mode=compile mpicc<br>-DHAVE_CONFIG_H <br>>>> -I. -I../../src -I/usr/include/libxml2 -I../../include <br>>>> -DGMXLIBDIR=\"/usr/local/gromacs/share/top\"
<br>-O3<br>>>> <br>>>> <br>>> -fomit-frame-pointer <br>>> <br>>> <br>>>> -finline-functions -Wall-Wno-unused -funroll-all-loops -MT<br>qm_mopac.lo<br>>>> <br>><br>> <br>>>> -MD -MP -MF .deps/qm_mopac.Tpo -c -o qm_mopac.lo qm_mopac.c<br>>>> mpicc -DHAVE_CONFIG_H -I. -I../../src -I/usr/include/libxml2 <br>>>> -I../../include<br>>>> <br>>>> <br>>> -DGMXLIBDIR=\"/usr/local/gromacs/share/top\" -O3 <br>>> <br>>> <br>>>> -fomit-frame-pointer -finline-functions -Wall -Wno-unused <br>>>> -funroll-all-loops -MT qm_mopac.lo -MD -MP -MF .deps/qm_mopac.Tpo<br>-c <br>>>> qm_mopac.c -o qm_mopac.o<br>>>> qm_mopac.c:52:17: error: nsb.h: Arquivo ou<br>diretório não<br>>>> <br>> encontrado<br>> <br>>>>
<br>>>> <br>>> My Portuguese is not so hot, but I figure this error translates as <br>>> "nsb.h: File or directory not found". That means what it<br>says.<br>>> GROMACS <br>>> version 3.3.x had this file, version 4.x doesn't. I had a look at <br>>> qm_mopac.c and I don't think it was using any of the contents of<br>>> <br>> nsb.h, <br>> <br>>> so you should be safe to remove this line from qm_mopac.c. Do let us <br>>> know how you get on.<br>>><br>>> Mark<br>>> <br>><br>><br>><br>> Veja quais são os assuntos do momento no Yahoo! +Buscados<br>> http://br.maisbuscados.yahoo.com<br>> -------------- next part --------------<br>> An HTML attachment was scrubbed...<br>> URL:<br>http://www.gromacs.org/pipermail/gmx-users/attachments/20081211/e9edd2ea/attachment.html<br>><br>> ------------------------------<br>><br>>
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