I used Ubuntu 12.10 64bit and gcc version 4.6.3. When I try to use the precompiled version of libmopac.a give me this error: /usr/bin/ld: skipping incompatible /home/raul/lib/libmopac.a when searching for -lmopac /usr/bin/ld: cannot find -lmopac collect2: ld returned 1 exit status
when I used this configure: ./configure --enable-mpi --prefix=/home/raul/gromacs_mopac LIBS="-lmopac -lgfortran" LDFLAGS=-L/home/raul/lib -L/home/raul/fftw/lib CPPFLAGS=-DUSE_MOPAC -I/home/raul/fftw/include --with-fft=fftw3 --disable-float --with-qmmm-mopac Installation is fine!! In the calculation of qmmm, Gromacs try searching the libraries of qm from gaussian. Whe I use AM1 method, give me this error: Program mdrun_d, VERSION 4.5.5 Source code file: qm_gaussian.c, line: 913 Fatal error: Call to '(null)/(null) < input.com > input.log' failed But, when i use RHF method, gave me other error: QM/MM calculation requested. there we go! Layer 0 nr of QM atoms 22 QMlevel: RHF/3-21G* number of CPUs for gaussian = 1 memory for gaussian = 50000000 accuracy in l510 = 8 NOT using cp-mcscf in l1003 Level of SA at start = 0 [raulxbsrk001:00965] *** Process received signal *** [raulxbsrk001:00965] Signal: Segmentation fault (11) [raulxbsrk001:00965] Signal code: Address not mapped (1) [raulxbsrk001:00965] Failing at address: (nil) [raulxbsrk001:00965] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0) [0x7fbaa74c1cb0] [raulxbsrk001:00965] [ 1] /lib/x86_64-linux-gnu/libc.so.6(+0x89101) [0x7fbaa717c101] [raulxbsrk001:00965] [ 2] /lib/x86_64-linux-gnu/libc.so.6(fputs+0x1e) [0x7fbaa716256e] [raulxbsrk001:00965] [ 3] /home/raul/gromacs_mopac/lib/libmd_mpi_d.so.6(init_gaussian+0x48f) [0x7fbaa838cd1f] [raulxbsrk001:00965] [ 4] /home/raul/gromacs_mopac/lib/libmd_mpi_d.so.6(init_QMMMrec+0x135c) [0x7fbaa837cbec] [raulxbsrk001:00965] [ 5] /home/raul/gromacs_mopac/bin/mdrun_d(mdrunner+0x1269) [0x41e6d9] [raulxbsrk001:00965] [ 6] /home/raul/gromacs_mopac/bin/mdrun_d(main+0x142e) [0x406bee] [raulxbsrk001:00965] [ 7] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) [0x7fbaa711476d] [raulxbsrk001:00965] [ 8] /home/raul/gromacs_mopac/bin/mdrun_d() [0x406e8d] [raulxbsrk001:00965] *** End of error message *** Violación de segmento (`core' generado) Thank you very much for your patience and intentions to help me > From: j...@um.es > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Gromacs + Mopac error > Date: Thu, 10 Jan 2013 14:32:43 +0000 > > Hi Raul > > I'd need to see the exact errors you get to be able to help you, and > other info such as which OS and compilers are you using. From your > previous post, it seemed that the mopac interface was not being compiled > with gromacs, but gaussian or orca ones were, according to the errors > you showed (note they mention "gaussian.c" and "qm_orca.c") > > The steps in the gromacs web should work (note you have to change some > files), and if not you can also try the precompiled library (libmopac.a, > in the same page). If you want to compile it by yourself, you can get > MOPAC code from http://openmopac.net/Downloads/Downloads.html (select > MOPAC7). Still, there might be some issues when compiling libmopac or in > runtime, but in such a case, we'd need to see what actual > errors/warnings are you observing (in your last mail it looked like the > installation went perfectly). > > Additionally, in case it could be of some help, I reported a > installation of gromacs-mopac in this mailing list some time ago > http://lists.gromacs.org/pipermail/gmx-users/2011-November/066133.html > > Try all that and report back if you encounter any problem > > Javier > > > El 10/01/13 14:59, raul arias escribió: > > Hi Javier, > > Thanks for your answer. > > I apologize for the delay in responding, but it's better with orca compiled > > version. > > Now I'm trying to compile with mopac again, but I think that my mistake is > > how to compile mopac. > > I'm following the steps of: > > http://www.gromacs.org/Documentation/Installation_Instructions_4.5/compiling_QMMM > > > > > > But in the version mopac7-1.11 has a subdirectory called "fortran" where > > the codes are. > > Also, here mopac.f file does not exist, but if the file mopac7app.f (I have > > to delete this? Like as deriv.f and moldat.f files) > > Can you help me at that point? > > > > > >> From: j...@um.es > >> To: gmx-users@gromacs.org > >> Subject: Re: [gmx-users] Gromacs + Mopac error > >> Date: Tue, 8 Jan 2013 08:59:31 +0000 > >> > >> Hi > >> > >> The problem is that in your first try the gaussian interface is being > >> used, while in the second the orca interface is used. > >> > >> The first try should have used the mopac interface but it apparently > >> ignored it, the reason why must be written in the configure output. > >> Could you show the last lines of such output? or clean the installation > >> directory and try again configure (using the options you mentioned > >> first, or you can add both --withoiut-qmmm-gaussian --with-qmmm-mopac) + > >> make + make install and provide the last lines of each output? > >> > >> Javier > >> > >> El 07/01/13 19:03, raul arias escribió: > >>> I'm trying to compile Gromacs with mopac using the instructions in the > >>> tutorial > >>> (the compilation of mopac was made with gfortran since f77 gave me error) > >>> > >>> ./configure --prefix=/home/raul/gromacs_mopac LIBS=-lmopac > >>> LDFLAGS="-L/home/raul/fftw/lib -L/home/raul/lib" CPPFLAGS="-DUSE_MOPAC > >>> -I/home/raul/fftw/include" --enable-mpi --disable-float --with-fft=fftw3 > >>> --with-qmmm-mopac > >>> > >>> everything is gone fine, but when I tried to run my simulation AM1, gave > >>> me this error: > >>> > >>> starting mdrun 'PHOTOACTIVE YELLOW PROTEIN' > >>> 5000 steps, 5.0 ps. > >>> nr mm atoms in gaussian.c = 3027 > >>> Calling '(null)/(null) < input.com > input.log' > >>> sh: 1: Syntax error: word unexpected > >>> ------------------------------------------------------- > >>> Program mdrun_d, VERSION 4.5.5 > >>> Source code file: qm_gaussian.c, line: 913 > >>> Fatal error: > >>> Call to '(null)/(null) < input.com > input.log' failed > >>> > >>> > >>> when I try to compile with the option: --without-qmmm-gaussian > >>> The error change to: > >>> > >>> starting mdrun 'PHOTOACTIVE YELLOW PROTEIN' > >>> 5000 steps, 5.0 ps. > >>> No information on the calculation given in <(null).ORCAINFO> > >>> ------------------------------------------------------- > >>> Program mdrun_d, VERSION 4.5.5 > >>> Source code file: qm_orca.c, line: 144 > >>> > >>> Routine should not have been called: > >>> qm_orca.c > >>> > >>> > >>> Any suggestions for my problem! > >>> > >>> Thank you. > >>> -- > >>> gmx-users mailing list gmx-users@gromacs.org > >>> http://lists.gromacs.org/mailman/listinfo/gmx-users > >>> * Please search the archive at > >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > >>> * Please don't post (un)subscribe requests to the list. Use the > >>> www interface or send it to gmx-users-requ...@gromacs.org. > >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> -- > >> Javier CEREZO BASTIDA > >> Ph.D. Student > >> Physical Chemistry > >> Universidad de Murcia > >> 30100, Murcia (SPAIN) > >> T: (0034)868887434 > >> > >> -- > >> gmx-users mailing list gmx-users@gromacs.org > >> http://lists.gromacs.org/mailman/listinfo/gmx-users > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > >> * Please don't post (un)subscribe requests to the list. Use the > >> www interface or send it to gmx-users-requ...@gromacs.org. > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- > Javier CEREZO BASTIDA > Ph.D. Student > Physical Chemistry > Universidad de Murcia > 30100, Murcia (SPAIN) > T: (0034)868887434 > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
