<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Very very thank you sir;<br>further when i run Mdrun after energy minimisatins by following command<br><span style="font-weight: bold;">./mdrun_d -s spep_em.tpr -o spep_em.trr -c spep_b4pr.gro -g em.log </span><br>I got errror as follows i am using<span style="font-weight: bold;"> Mopac/gromac</span>s intrface<br>QM/MM calculation requested.<br>there we go!<br>Layer 0<br>nr of QM atoms 14<br>QMlevel: MP2/STO-3G<br><br><span style="font-weight: bold;">number of CPUs for gaussian = 1</span><br style="font-weight: bold;"><span style="font-weight: bold;">memory for gaussian = 50000000</span><br style="font-weight: bold;"><span style="font-weight: bold;">accuracy in l510 = 8</span><br style="font-weight: bold;"><span style="font-weight: bold;">NOT using cp-mcscf in l1003</span><br style="font-weight: bold;"><span style="font-weight: bold;">Level of SA at start =
0</span><br style="font-weight: bold;"><span style="font-weight: bold;">Segmentation fault (core dumped)</span><br>what could i do to rectify this error i am expecting you<span style="font-weight: bold;">r gem of reply</span><br><br><br>--- On <b>Tue, 21/9/10, Gerrit Groenhof <i><ggroenh@gwdg.de></i></b> wrote:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>From: Gerrit Groenhof <ggroenh@gwdg.de><br>Subject: [gmx-users] QM/MM topology fiels problem<br>To: gmx-users@gromacs.org<br>Date: Tuesday, 21 September, 2010, 4:16 PM<br><br><div class="plainMail"> Please read the error message: it says that you need no parameters for <br>your conn bonds.<br><br>Gerrit<br><br><br><br><br>> Message: 2<br>> Date: Tue, 21 Sep 2010 14:58:40 +0530 (IST)<br>> From: vidhya sankar<<a ymailto="mailto:scvsankar_agr@yahoo.com"
href="/mc/compose?to=scvsankar_agr@yahoo.com">scvsankar_agr@yahoo.com</a>><br>> Subject: [gmx-users] QM/MM topology fiels problem<br>> To: <a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> Message-ID:<<a ymailto="mailto:277598.19746.qm@web95503.mail.in.yahoo.com" href="/mc/compose?to=277598.19746.qm@web95503.mail.in.yahoo.com">277598.19746.qm@web95503.mail.in.yahoo.com</a>><br>> Content-Type: text/plain; charset="utf-8"<br>><br>> Dear gromacs users , thank you for your reply<br>> when i run the<br>> ./grompp it shows the error as follows<br>> ./grompp_d -f em.mdp -c spep_b4em.gro -p spep.top -o spep_em.tpr<br>><br>> ignoring obsolete mdp entry 'cpp'<br>><br>> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.4#<br>> checking input for internal consistency...<br>> processing topology...<br>>
Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6.itp<br>> Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6nb.itp<br>> Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6bon.itp<br>> Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp<br>> Generated 222 of the 1653 non-bonded parameter combinations<br>> -------------------------------------------------------<br>> Program grompp_d, VERSION 4.0.7<br>> Source code file: toppush.c, line: 1379<br>><br>> Fatal error:<br>> Incorrect number of parameters - found 2, expected 0 or 0 for Connect Bonds<br>> what could i do to avod error? i am expecting your valuable reply<br>><br>><br>> -------------- next part --------------<br>> An HTML attachment was scrubbed...<br>> URL: <a href="http://lists.gromacs.org/pipermail/gmx-users/attachments/20100921/ece4e258/attachment-0001.html"
target="_blank">http://lists.gromacs.org/pipermail/gmx-users/attachments/20100921/ece4e258/attachment-0001.html</a><br>><br>> ------------------------------<br>><br>> Message: 3<br>> Date: Tue, 21 Sep 2010 11:57:22 +0200 (MEST)<br>> From: Fabio Affinito<<a ymailto="mailto:f.affinito@cineca.it" href="/mc/compose?to=f.affinito@cineca.it">f.affinito@cineca.it</a>><br>> Subject: Re: [gmx-users] error on compilation on BlueGene/P<br>> To: Discussion list for GROMACS users<<a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> Message-ID:<<a ymailto="mailto:4C988143.9020807@cineca.it" href="/mc/compose?to=4C988143.9020807@cineca.it">4C988143.9020807@cineca.it</a>><br>> Content-Type: text/plain; charset=ISO-8859-1<br>><br>> Like for the frontend, the --enable-fortran is the problem.<br>> Maybe it could be useful to update the instruction page
:)<br>><br>> Fabio<br>><br>><br>> On 09/21/2010 10:54 AM, Mark Abraham wrote:<br>>><br>>> ----- Original Message -----<br>>> From: Fabio Affinito<<a ymailto="mailto:f.affinito@cineca.it" href="/mc/compose?to=f.affinito@cineca.it">f.affinito@cineca.it</a>><br>>> Date: Tuesday, September 21, 2010 18:51<br>>> Subject: Re: [gmx-users] error on compilation on BlueGene/P<br>>> To: Discussion list for GROMACS users<<a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>>><br>>>> Thank you, Mark and Berk!<br>>>> your suggestion was helpful and I successfully compiled on the<br>>>> frontend.Now I have a problem when I compile on the compute nodes.<br>>>> Configure was fine with these parameters:<br>>>><br>>>> ../configure --prefix=/bgp/userinternal/cin0644a/gromacs
\<br>>>> --host=ppc --build=ppc64 --enable-ppc-sqrt=1 \<br>>>> --disable-ppc-altivec \<br>>>> --enable-bluegene --enable-fortran --enable-mpi \<br>>>> --with-fft=fftw3 \<br>>>> --program-suffix=_mpi_bg \<br>>>> --without-x \<br>>>> CC=mpixlc_r \<br>>>> CFLAGS="-O3 -qarch=450d -qtune=450" \<br>>>> MPICC=mpixlc_r CXX=mpixlC_r \<br>>>>
CXXFLAGS="-O3 -qarch=450d -qtune=450" \<br>>>> CPPFLAGS="-I/bgp/userinternal/cin0644a/fftwlibs/include" \<br>>>> F77=mpixlf77_r FFLAGS="-O3 -qarch=auto -qtune=auto" \<br>>>> LDFLAGS="-L/bgp/userinternal/cin0644a/fftwlibs/lib" \<br>>>> LIBS="-lmass"<br>>>><br>>>> But when I compile using "make mdrun" the compilation stops in<br>>>> this way.<br>>>><br>>>> creating libgmxpreprocess_mpi.la<br>>>> (cd .libs&& rm -f libgmxpreprocess_mpi.la&& ln -s<br>>>> ../libgmxpreprocess_mpi.la libgmxpreprocess_mpi.la)<br>>>> make[1]: *** No rule to make target
`../mdlib/libmd_mpi.la',<br>>>> needed by<br>>>> `mdrun'. Stop.<br>>>> make[1]: Leaving directory<br>>>> `/bgp/userinternal/cin0644a/gmx/bgp/src/kernel'<br>>>> Any suggestion? Thanks!<br>>><br>>> Normally that would be symptomatic of an earlier error in make (or maybe<br>>> configure). Please check carefully.<br>>><br>>> Mark<br>>><br>><br><br>-- <br>gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>Please don't post (un)subscribe requests to the list.
Use the <br>www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="/mc/compose?to=gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br></div></blockquote></td></tr></table><br>