[gmx-users] REg QM/MM Mdrun error

[vidhya sankar]

Very very thank you sir;
further when i run Mdrun after energy minimisatins by following command
./mdrun_d -s spep_em.tpr -o spep_em.trr -c spep_b4pr.gro -g em.log 
I got errror as follows i am using Mopac/gromacs intrface
QM/MM calculation requested.
there we go!
Layer 0
nr of QM atoms 14
QMlevel: MP2/STO-3G

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
Segmentation fault (core dumped)
what could i do to rectify this error i am expecting your gem of reply


--- On Tue, 21/9/10, Gerrit Groenhof <ggroenh at gwdg.de> wrote:

From: Gerrit Groenhof <ggroenh at gwdg.de>
Subject: [gmx-users] QM/MM topology fiels problem
To: gmx-users at gromacs.org
Date: Tuesday, 21 September, 2010, 4:16 PM

  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_agr at yahoo.com>
> Subject: [gmx-users] QM/MM topology fiels problem
> To: gmx-users at gromacs.org
> Message-ID:<277598.19746.qm at 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.affinito at cineca.it>
> Subject: Re: [gmx-users] error on compilation on BlueGene/P
> To: Discussion list for GROMACS users<gmx-users at gromacs.org>
> Message-ID:<4C988143.9020807 at 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.affinito at 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 at 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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