FW: [gmx-users] Gromacs + Mopac error

raul arias rarias at alumnos.utalca.cl
Thu Jan 10 16:45:51 CET 2013 

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: jcb1 at um.es
> To: gmx-users at 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: jcb1 at um.es
> >> To: gmx-users at 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 at 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-request at 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 at 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-request at gromacs.org.
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >>
> >   		 	   		  --
> > gmx-users mailing list    gmx-users at 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-request at 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 at 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-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
>

More information about the gromacs.org_gmx-users mailing list