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 <[email protected]> wrote: From: Gerrit Groenhof <[email protected]> Subject: [gmx-users] QM/MM topology fiels problem To: [email protected] 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<[email protected]> > Subject: [gmx-users] QM/MM topology fiels problem > To: [email protected] > Message-ID:<[email protected]> > 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 > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20100921/ece4e258/attachment-0001.html > > ------------------------------ > > Message: 3 > Date: Tue, 21 Sep 2010 11:57:22 +0200 (MEST) > From: Fabio Affinito<[email protected]> > Subject: Re: [gmx-users] error on compilation on BlueGene/P > To: Discussion list for GROMACS users<[email protected]> > Message-ID:<[email protected]> > 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<[email protected]> >> Date: Tuesday, September 21, 2010 18:51 >> Subject: Re: [gmx-users] error on compilation on BlueGene/P >> To: Discussion list for GROMACS users<[email protected]> >> >>> 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 >> > -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
