There is one point you have to note: although the qmmm interface of
gromacs can be applied with different codes (gaussian, orca, mopac..),
only ONE must be selected at compilation. That is, if you have a mdrun
binary compiled with gaussian-qmmm, all qmmm computations will use the
gaussian interface.
So, according to the error in the output, specifically at:
Program mdrun_d, VERSION 4.5.5
Source code file: qm_gaussian.c, line: 913
It is observed that your installation was done with with the gaussian
interface (that's what qm_gaussian.c is) not with mopac. Since in order
to use the gaussian interface you need to meet some requirements (i.e.
to have a specifically modified gaussian binary) you obtain an error as
you are experiencing.
So, even if you think the installation is correct, something is not
going well. I remember that special caution had to be taken if you first
configure --with-qmmm-gaussian (this is the default) and then you try to
compile again with other qmmm interface. So, "make clean" is required
prior to a new installation. To sum up again: you have to realize that
something strange is going on, since even if you include
--with-qmmm-mopac, the gaussian interface is being used, and the first
step to solve your problem is to be sure that you make your installation
with mopac (not gaussian). Try "make clean" the directory, adding
--without-qmmm-gaussian... Also inspect the output of configure to see
why gaussian interface is used.
Javier
El 10/01/13 16:45, raul arias escribió:
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: [email protected]
To: [email protected]
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: [email protected]
To: [email protected]
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.
--
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Javier CEREZO BASTIDA
Ph.D. Student
Physical Chemistry
Universidad de Murcia
30100, Murcia (SPAIN)
T: (0034)868887434
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--
Javier CEREZO BASTIDA
Ph.D. Student
Physical Chemistry
Universidad de Murcia
30100, Murcia (SPAIN)
T: (0034)868887434
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
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--
Javier CEREZO BASTIDA
Ph.D. Student
Physical Chemistry
Universidad de Murcia
30100, Murcia (SPAIN)
T: (0034)868887434
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
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