Please read the error message: it says that you need no parameters for
your conn bonds.
Gerrit
Message: 2
Date: Tue, 21 Sep 2010 14:58:40 +0530 (IST)
From: vidhya sankar<scvsankar_...@yahoo.com>
Subject: [gmx-users] QM/MM topology fiels problem
To: gmx-users@gromacs.org
Message-ID:<277598.19746...@web95503.mail.in.yahoo.com>
Content-Type: text/plain; charset="utf-8"
Dear gromacs users , thank you for your reply
when i run the
./grompp it shows the error as follows
./grompp_d -f em.mdp -c spep_b4em.gro -p spep.top -o spep_em.tpr
ignoring obsolete mdp entry 'cpp'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.4#
checking input for internal consistency...
processing topology...
Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6nb.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6bon.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp
Generated 222 of the 1653 non-bonded parameter combinations
-------------------------------------------------------
Program grompp_d, VERSION 4.0.7
Source code file: toppush.c, line: 1379
Fatal error:
Incorrect number of parameters - found 2, expected 0 or 0 for Connect Bonds
what could i do to avod error? i am expecting your valuable reply
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Message: 3
Date: Tue, 21 Sep 2010 11:57:22 +0200 (MEST)
From: Fabio Affinito<f.affin...@cineca.it>
Subject: Re: [gmx-users] error on compilation on BlueGene/P
To: Discussion list for GROMACS users<gmx-users@gromacs.org>
Message-ID:<4c988143.9020...@cineca.it>
Content-Type: text/plain; charset=ISO-8859-1
Like for the frontend, the --enable-fortran is the problem.
Maybe it could be useful to update the instruction page :)
Fabio
On 09/21/2010 10:54 AM, Mark Abraham wrote:
----- Original Message -----
From: Fabio Affinito<f.affin...@cineca.it>
Date: Tuesday, September 21, 2010 18:51
Subject: Re: [gmx-users] error on compilation on BlueGene/P
To: Discussion list for GROMACS users<gmx-users@gromacs.org>
Thank you, Mark and Berk!
your suggestion was helpful and I successfully compiled on the
frontend.Now I have a problem when I compile on the compute nodes.
Configure was fine with these parameters:
../configure --prefix=/bgp/userinternal/cin0644a/gromacs \
--host=ppc --build=ppc64 --enable-ppc-sqrt=1 \
--disable-ppc-altivec \
--enable-bluegene --enable-fortran --enable-mpi \
--with-fft=fftw3 \
--program-suffix=_mpi_bg \
--without-x \
CC=mpixlc_r \
CFLAGS="-O3 -qarch=450d -qtune=450" \
MPICC=mpixlc_r CXX=mpixlC_r \
CXXFLAGS="-O3 -qarch=450d -qtune=450" \
CPPFLAGS="-I/bgp/userinternal/cin0644a/fftwlibs/include" \
F77=mpixlf77_r FFLAGS="-O3 -qarch=auto -qtune=auto" \
LDFLAGS="-L/bgp/userinternal/cin0644a/fftwlibs/lib" \
LIBS="-lmass"
But when I compile using "make mdrun" the compilation stops in
this way.
creating libgmxpreprocess_mpi.la
(cd .libs&& rm -f libgmxpreprocess_mpi.la&& ln -s
../libgmxpreprocess_mpi.la libgmxpreprocess_mpi.la)
make[1]: *** No rule to make target `../mdlib/libmd_mpi.la',
needed by
`mdrun'. Stop.
make[1]: Leaving directory
`/bgp/userinternal/cin0644a/gmx/bgp/src/kernel'
Any suggestion? Thanks!
Normally that would be symptomatic of an earlier error in make (or maybe
configure). Please check carefully.
Mark
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