<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><DIV>Thank you for your suggest, my gromacs reinstalled: ./configure --<BR>--without-qmmm-gaussian --without-qmmm-orca ....</DIV>
<DIV> </DIV>
<DIV>when mpirun -np 1 mdrun_p -v -s pyp_qm.tpr, </DIV>
<DIV><BR>Back Off! I just backed up md.log to ./#md.log.1#<BR>Getting Loaded...<BR>Reading file pyp_qm.tpr, VERSION 4.5.3 (double precision)<BR>Loaded with Money</DIV>
<DIV>QM/MM calculation requested.<BR>there we go!<BR>Layer 0<BR>nr of QM atoms 22<BR>QMlevel: RHF/3-21G</DIV>
<DIV>/home/user/orca_x86_64_exe_r2131/home/user/orca_x86_64_exe_r2131...<BR>orca initialised...</DIV>
<DIV>Back Off! I just backed up traj.trr to ./#traj.trr.1#</DIV>
<DIV>Back Off! I just backed up traj.xtc to ./#traj.xtc.1#</DIV>
<DIV>Back Off! I just backed up ener.edr to ./#ener.edr.1#<BR>starting mdrun 'PHOTOACTIVE YELLOW PROTEIN in water'<BR>500 steps, 0.5 ps.</DIV>
<DIV>Calling '/home/user/orca_x86_64_exe_r2131/orca pyp_qm.inp >> pyp_qm.out'<BR> Unless this is specifically allowed this means that the basis set is not <BR> available for this element - Aborting the run</DIV>
<DIV>-------------------------------------------------------<BR>Program mdrun_p, VERSION 4.5.3<BR>Source code file: qm_orca.c, line: 409</DIV>
<DIV>Fatal error:<BR>Call to '/home/user/orca_x86_64_exe_r2131/orca pyp_qm.inp >> pyp_qm.out' failed</DIV>
<DIV>......</DIV>
<DIV>but a question raised: how to deal with LA in the QMatoms in orca inputfile? using DA ( dummy atom in the ORCA) repaces LA in the QMatoms in the gromacs ?</DIV>
<DIV>please give me a suggestion!</DIV>
<DIV>Thank you!<BR><A class=plink href="http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844" rel=nofollow target=_blank><IMG class=pimg border=0 alt=4 src="http://opi.yahoo.com/online?u=zhaoxiitc2002&t=4&l=cn"></A><BR><BR>--- <B>11年11月7日,周一, Micha Ben Achim Kunze <I><ucbtmbk@live.ucl.ac.uk></I></B> 写道:<BR></DIV>
<BLOCKQUOTE style="BORDER-LEFT: rgb(16,16,255) 2px solid; PADDING-LEFT: 5px; MARGIN-LEFT: 5px"><BR>发件人: Micha Ben Achim Kunze <ucbtmbk@live.ucl.ac.uk><BR>主题: Re: 回复: [gmx-users] Re 1. orca and qm/mm (xi zhao)<BR>收件人: gmx-users@gromacs.org<BR>日期: 2011年11月7日,周一,下午10:50<BR><BR>
<DIV id=yiv1828806674>
<DIV>From the output it looks like you forgot the --without-qmmm-gaussian flag while compiling.<BR><BR>Micha<BR>On 07/11/11 14:42, xi zhao wrote:
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<DIV>When remove these lines, the errros still :Fatal error:<BR>Invalid QMMM input: 1 groups 0 basissets and 0 methods;</DIV>
<DIV>when put something there, (<BR>QMmethod =rhf;QMbasis =sto-3g), <BR><BR>grompp_a -f pyp.mdp -c pyp.gro -p pyp.top -n pyp.ndx -o pyp_qm.tpr -maxwarn 10</DIV>
<DIV> </DIV>
<DIV>mpirun -np 8 mdrun_a -v -s pyp_qm.tpr </DIV>
<DIV>......</DIV>
<DIV>Back Off! I just backed up md.log to ./#md.log.7#<BR>Getting Loaded...<BR>Reading file pyp_qm.tpr, VERSION 4.5.3 (double precision)<BR>Loaded with Money</DIV>
<DIV>QM/MM calculation requested.<BR>QM/MM calculation requested.<BR>QM/MM calculation requested.<BR>QM/MM calculation requested.<BR>QM/MM calculation requested.<BR>QM/MM calculation requested.<BR>there we go!<BR>QM/MM calculation requested.<BR>QM/MM calculation requested.<BR>there we go!<BR>there we go!<BR>there we go!<BR>there we go!<BR>there we go!<BR>there we go!<BR>there we go!<BR>Layer 0<BR>nr of QM atoms 22<BR>QMlevel: RHF/STO-3G</DIV>
<DIV>number of CPUs for gaussian = 1<BR>memory for gaussian = 50000000<BR>accuracy in l510 = 8<BR>NOT using cp-mcscf in l1003<BR>Level of SA at start = 0<BR>-----------------------------------------------------------------------------<BR>One of the processes started by mpirun has exited with a nonzero exit<BR>code. This typically indicates that the process finished in error.<BR>If your process did not finish in error, be sure to include a "return<BR>0" or "exit(0)" in your C code before exiting the application.</DIV>
<DIV>PID 11786 failed on node n0 (127.0.0.1) due to signal 11.</DIV>
<DIV> </DIV>
<DIV>how to deal with?</DIV>
<DIV><A class=yiv1828806674plink href="http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844" rel=nofollow target=_blank><IMG class=yiv1828806674pimg border=0 alt=4 src="http://opi.yahoo.com/online?u=zhaoxiitc2002&t=4&l=cn"></A><BR>--- <B>11年11月7日,周一, Gerrit Groenhof <I><A class=yiv1828806674moz-txt-link-rfc2396E href="http://cn.mc151.mail.yahoo.com/mc/compose?to=ggroenh@gwdg.de" rel=nofollow target=_blank ymailto="mailto:ggroenh@gwdg.de"><ggroenh@gwdg.de></A></I></B> 写道:<BR></DIV>
<BLOCKQUOTE style="BORDER-LEFT: rgb(16,16,255) 2px solid; PADDING-LEFT: 5px; MARGIN-LEFT: 5px"><BR>发件人: Gerrit Groenhof <A class=yiv1828806674moz-txt-link-rfc2396E href="http://cn.mc151.mail.yahoo.com/mc/compose?to=ggroenh@gwdg.de" rel=nofollow target=_blank ymailto="mailto:ggroenh@gwdg.de"><ggroenh@gwdg.de></A><BR>主题: [gmx-users] Re 1. orca and qm/mm (xi zhao)<BR>收件人: <A class=yiv1828806674moz-txt-link-abbreviated href="http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org" rel=nofollow target=_blank ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR>日期: 2011年11月7日,周一,下午9:23<BR><BR>
<DIV class=yiv1828806674plainMail>Try to remove these lines, or put something there. The input is ignored, but since strings are used as input (for use in multui-layer oniom), leaving blank causes an error.<BR><BR>Gerrit<BR>On 7 Nov 2011, at 14:21, <A href="http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org" rel=nofollow target=_blank>gmx-users-request@gromacs.org</A> wrote:<BR><BR>> Send gmx-users mailing list submissions to<BR>> <A href="http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org" rel=nofollow target=_blank>gmx-users@gromacs.org</A><BR>> <BR>> To subscribe or unsubscribe via the World Wide Web, visit<BR>> <A href="http://lists.gromacs.org/mailman/listinfo/gmx-users" rel=nofollow target=_blank>http://lists.gromacs.org/mailman/listinfo/gmx-users</A><BR>> or, via email, send a message with subject or body 'help' to<BR>> <A
href="http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org" rel=nofollow target=_blank>gmx-users-request@gromacs.org</A><BR>> <BR>> You can reach the person managing the list at<BR>> <A href="http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-owner@gromacs.org" rel=nofollow target=_blank>gmx-users-owner@gromacs.org</A><BR>> <BR>> When replying, please edit your Subject line so it is more specific<BR>> than "Re: Contents of gmx-users digest..."<BR>> <BR>> <BR>> Today's Topics:<BR>> <BR>> 1. orca and qm/mm (xi zhao)<BR>> <BR>> <BR>> ----------------------------------------------------------------------<BR>> <BR>> Message: 1<BR>> Date: Mon, 7 Nov 2011 20:54:04 +0800 (CST)<BR>> From: xi zhao <<A href="http://cn.mc151.mail.yahoo.com/mc/compose?to=zhaoxiitc2002@yahoo.com.cn" rel=nofollow
target=_blank>zhaoxiitc2002@yahoo.com.cn</A>><BR>> Subject: [gmx-users] orca and qm/mm<BR>> To: <A href="http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org" rel=nofollow target=_blank>gmx-users@gromacs.org</A><BR>> Message-ID:<BR>> <<A href="http://cn.mc151.mail.yahoo.com/mc/compose?to=1320670444.82465.YahooMailClassic@web15103.mail.cnb.yahoo.com" rel=nofollow target=_blank>1320670444.82465.YahooMailClassic@web15103.mail.cnb.yahoo.com</A>><BR>> Content-Type: text/plain; charset="utf-8"<BR>> <BR>> All users:<BR>> <BR>> <BR>> According to <A href="http://wwwuser.gwdg.de/~ggroenh/qmmm.html#code" rel=nofollow target=_blank>http://wwwuser.gwdg.de/~ggroenh/qmmm.html#code</A>, I want to build qm/mm calculation by using gromacs 4.5.3 + orca 2.8.0. I set up the BASENAME, ORCA_PATH and BASENAME.ORCAINFO as told in the instruction. <BR>> BASENAME=pyp_qm<BR>> here is the
BASENAME.ORCAINFO file:<BR>> ! RKS B3LYP/G SV(P) TightSCF Opt<BR>> <BR>> here is the md file:<BR>> integrator = md<BR>> tinit = 0<BR>> dt = 0.001<BR>> nsteps = 500<BR>> nstcomm = 1<BR>> comm_grps = system<BR>> <BR>> emtol = 100.0<BR>> emstep = 0.001<BR>> nstcgsteep = 50<BR>> <BR>> nstxout
= 1<BR>> nstvout = 1<BR>> nstfout = 1<BR>> nstlog = 1<BR>> nstenergy = 1<BR>> nstxtcout = 1<BR>> xtc_grps = system<BR>> energygrps = QMatoms rest_Protein SOL<BR>> <BR>> nstlist = 10<BR>> ns_type = grid<BR>> pbc = xyz<BR>> rlist
= 1.0<BR>> <BR>> coulombtype = cut-off<BR>> rcoulomb = 1.4<BR>> epsilon_r = 1<BR>> vdwtype = Cut-off<BR>> rvdw = 1.4<BR>> <BR>> tcoupl = berendsen<BR>> tc-grps = rest_Protein SOL QMatoms<BR>> tau_t = 0.1 0.1 0 ; QM atoms are uncoupled<BR>> ref_t = 300 300 300<BR>>
Pcoupl = Berendsen<BR>> pcoupltype = isotropic<BR>> tau_p = 1.0<BR>> compressibility = 4.5e-5<BR>> ref_p = 1.0<BR>> <BR>> free_energy = no<BR>> init_lambda = 0<BR>> delta_lambda = 0<BR>> QMMM = yes<BR>> QMMM-grps = QMatoms<BR>> QMmethod =<BR>> QMbasis
=<BR>> QMMMscheme = normal<BR>> QMcharge = -1<BR>> CASelectrons =<BR>> CASorbitals =<BR>> SH =<BR>> <BR>> gen_vel = no<BR>> gen_temp = 300<BR>> gen_seed = 173529<BR>> <BR>> constraints = all-bonds<BR>> constraint_algorithm = LINCS<BR>> unconstrained_start = yes<BR>>
shake_tol = 0.0001<BR>> lincs_order = 4<BR>> lincs_warnangle = 30<BR>> morse = no<BR>> According to the instruction “In the ORCAINFO-file the method, basis set and all other ORCA-specific keywords must be given. (This also means that QMmethod and QMbasis from the mdp-file are ignored).”, the QMmethod and QMbasis are blank, <BR>> But When grompp<BR>> grompp_c -f pyp.mdp -c pyp.gro -p pyp.top -n pyp.ndx -o pyp_qm.tpr<BR>> ……….<BR>> Fatal error:<BR>> Invalid QMMM input: 1 groups 0 basissets and 0 methods.<BR>> <BR>> How to deal with it? Please help me!<BR>> <BR>> -------------- next part --------------<BR>> An HTML attachment was scrubbed...<BR>> URL: <A
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