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    I am not sure I understand exactly what you mean but this is all
    covered in Gerrit's QM/MM tutorials, I'd recommend you go through
    those. In the ORCA files there is no need to do anything with LAs,
    GMX will hand a file with the QMsubsystem to ORCA which includes the
    LA as hydrogens in your case I guess.<br>
    <br>
    Cheers,<br>
    Micha<br>
    On 08/11/11 07:07, xi zhao wrote:
    <blockquote
      cite="mid:1320736058.13600.YahooMailClassic@web15107.mail.cnb.yahoo.com"
      type="cite">
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              <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 &gt;&gt; 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 &gt;&gt; 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 moz-do-not-send="true" class="plink"
href="http://cn.webmessenger.yahoo.com/index.php?t=1&amp;to=eWlkPXpoYW94aWl0YzIwMDI-&amp;sig=703fa929658518b2720b087c59cd85f2dabf8844"
                  rel="nofollow" target="_blank"><img
                    moz-do-not-send="true" class="pimg" alt="4"
                    src="http://opi.yahoo.com/online?u=zhaoxiitc2002&amp;t=4&amp;l=cn"
                    border="0"></a><br>
                <br>
                --- <b>11年11月7日,周一, Micha Ben Achim Kunze <i><a class="moz-txt-link-rfc2396E" href="mailto:ucbtmbk@live.ucl.ac.uk">&lt;ucbtmbk@live.ucl.ac.uk&gt;</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: Micha Ben Achim Kunze
                <a class="moz-txt-link-rfc2396E" href="mailto:ucbtmbk@live.ucl.ac.uk">&lt;ucbtmbk@live.ucl.ac.uk&gt;</a><br>
                主题: Re: 回复: [gmx-users] Re 1. orca and qm/mm (xi zhao)<br>
                收件人: <a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><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:
                    <blockquote type="cite">
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                        <tbody>
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                            <td valign="top">
                              <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 moz-do-not-send="true"
                                  class="yiv1828806674plink"
href="http://cn.webmessenger.yahoo.com/index.php?t=1&amp;to=eWlkPXpoYW94aWl0YzIwMDI-&amp;sig=703fa929658518b2720b087c59cd85f2dabf8844"
                                  rel="nofollow" target="_blank"><img
                                    moz-do-not-send="true"
                                    class="yiv1828806674pimg" alt="4"
                                    src="http://opi.yahoo.com/online?u=zhaoxiitc2002&amp;t=4&amp;l=cn"
                                    border="0"></a><br>
                                --- <b>11年11月7日,周一, Gerrit Groenhof <i><a
                                      moz-do-not-send="true"
                                      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">&lt;ggroenh@gwdg.de&gt;</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
                                  moz-do-not-send="true"
                                  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">&lt;ggroenh@gwdg.de&gt;</a><br>
                                主题: [gmx-users] Re 1. orca and qm/mm (xi
                                zhao)<br>
                                收件人: <a moz-do-not-send="true"
                                  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
                                    moz-do-not-send="true"
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>
                                  &gt; Send gmx-users mailing list
                                  submissions to<br>
                                  &gt;     <a moz-do-not-send="true"
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                                  &gt; <br>
                                  &gt; To subscribe or unsubscribe via
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                                  &gt; or, via email, send a message
                                  with subject or body 'help' to<br>
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                                  the list at<br>
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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>
                                  &gt; <br>
                                  &gt; When replying, please edit your
                                  Subject line so it is more specific<br>
                                  &gt; than "Re: Contents of gmx-users
                                  digest..."<br>
                                  &gt; <br>
                                  &gt; <br>
                                  &gt; Today's Topics:<br>
                                  &gt; <br>
                                  &gt;   1. orca and qm/mm (xi zhao)<br>
                                  &gt; <br>
                                  &gt; <br>
                                  &gt;
                                  ----------------------------------------------------------------------<br>
                                  &gt; <br>
                                  &gt; Message: 1<br>
                                  &gt; Date: Mon, 7 Nov 2011 20:54:04
                                  +0800 (CST)<br>
                                  &gt; From: xi zhao &lt;<a
                                    moz-do-not-send="true"
href="http://cn.mc151.mail.yahoo.com/mc/compose?to=zhaoxiitc2002@yahoo.com.cn"
                                    rel="nofollow" target="_blank">zhaoxiitc2002@yahoo.com.cn</a>&gt;<br>
                                  &gt; Subject: [gmx-users] orca and
                                  qm/mm<br>
                                  &gt; To: <a moz-do-not-send="true"
href="http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org"
                                    rel="nofollow" target="_blank">gmx-users@gromacs.org</a><br>
                                  &gt; Message-ID:<br>
                                  &gt;     &lt;<a moz-do-not-send="true"
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>&gt;<br>
                                  &gt; Content-Type: text/plain;
                                  charset="utf-8"<br>
                                  &gt; <br>
                                  &gt; All users:<br>
                                  &gt; <br>
                                  &gt;  <br>
                                  &gt; According to <a
                                    moz-do-not-send="true"
                                    href="http://wwwuser.gwdg.de/%7Eggroenh/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>
                                  &gt; BASENAME=pyp_qm<br>
                                  &gt; here is the BASENAME.ORCAINFO
                                  file:<br>
                                  &gt; ! RKS B3LYP/G SV(P) TightSCF Opt<br>
                                  &gt;  <br>
                                  &gt; here is the md file:<br>
                                  &gt; integrator               = md<br>
                                  &gt; tinit                    = 0<br>
                                  &gt; dt                       = 0.001<br>
                                  &gt; nsteps                   = 500<br>
                                  &gt; nstcomm                  = 1<br>
                                  &gt; comm_grps                = system<br>
                                  &gt;  <br>
                                  &gt; emtol                    = 100.0<br>
                                  &gt; emstep                   = 0.001<br>
                                  &gt; nstcgsteep               = 50<br>
                                  &gt;  <br>
                                  &gt; nstxout                  = 1<br>
                                  &gt; nstvout                  = 1<br>
                                  &gt; nstfout                  = 1<br>
                                  &gt; nstlog                   = 1<br>
                                  &gt; nstenergy                = 1<br>
                                  &gt; nstxtcout                = 1<br>
                                  &gt; xtc_grps                 = system<br>
                                  &gt; energygrps               =
                                  QMatoms rest_Protein SOL<br>
                                  &gt;  <br>
                                  &gt; nstlist                  = 10<br>
                                  &gt; ns_type                  = grid<br>
                                  &gt; pbc                      = xyz<br>
                                  &gt; rlist                    = 1.0<br>
                                  &gt;  <br>
                                  &gt; coulombtype              =
                                  cut-off<br>
                                  &gt; rcoulomb                 = 1.4<br>
                                  &gt; epsilon_r                = 1<br>
                                  &gt; vdwtype                  =
                                  Cut-off<br>
                                  &gt; rvdw                     = 1.4<br>
                                  &gt;  <br>
                                  &gt; tcoupl                   =
                                  berendsen<br>
                                  &gt; tc-grps                  =
                                  rest_Protein SOL QMatoms<br>
                                  &gt; tau_t                    = 0.1
                                  0.1 0 ; QM atoms are uncoupled<br>
                                  &gt; ref_t                    = 300
                                  300 300<br>
                                  &gt; Pcoupl                   =
                                  Berendsen<br>
                                  &gt; pcoupltype               =
                                  isotropic<br>
                                  &gt; tau_p                    = 1.0<br>
                                  &gt; compressibility          = 4.5e-5<br>
                                  &gt; ref_p                    = 1.0<br>
                                  &gt;  <br>
                                  &gt; free_energy              = no<br>
                                  &gt; init_lambda              = 0<br>
                                  &gt; delta_lambda             = 0<br>
                                  &gt; QMMM                     = yes<br>
                                  &gt; QMMM-grps                =
                                  QMatoms<br>
                                  &gt; QMmethod                 =<br>
                                  &gt; QMbasis                  =<br>
                                  &gt; QMMMscheme               = normal<br>
                                  &gt; QMcharge                 = -1<br>
                                  &gt; CASelectrons             =<br>
                                  &gt; CASorbitals              =<br>
                                  &gt; SH                       =<br>
                                  &gt;  <br>
                                  &gt; gen_vel                  = no<br>
                                  &gt; gen_temp                 = 300<br>
                                  &gt; gen_seed                 = 173529<br>
                                  &gt;  <br>
                                  &gt; constraints              =
                                  all-bonds<br>
                                  &gt; constraint_algorithm     = LINCS<br>
                                  &gt; unconstrained_start      = yes<br>
                                  &gt; shake_tol                = 0.0001<br>
                                  &gt; lincs_order              = 4<br>
                                  &gt; lincs_warnangle          = 30<br>
                                  &gt; morse                    = no<br>
                                  &gt;   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>
                                  &gt;    But When grompp<br>
                                  &gt; grompp_c -f pyp.mdp -c pyp.gro -p
                                  pyp.top -n pyp.ndx -o pyp_qm.tpr<br>
                                  &gt; ……….<br>
                                  &gt; Fatal error:<br>
                                  &gt; Invalid QMMM input: 1 groups 0
                                  basissets and 0 methods.<br>
                                  &gt;  <br>
                                  &gt; How to deal with it? Please help
                                  me!<br>
                                  &gt; <br>
                                  &gt; -------------- next part
                                  --------------<br>
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                                  &gt; gmx-users mailing list<br>
                                  &gt; <a moz-do-not-send="true"
href="http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org"
                                    rel="nofollow" target="_blank">gmx-users@gromacs.org</a><br>
                                  &gt; <a moz-do-not-send="true"
                                    href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
                                    rel="nofollow" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
                                  &gt; Please search the archive at <a
                                    moz-do-not-send="true"
                                    href="http://www.gromacs.org/Support/Mailing_Lists/Search"
                                    rel="nofollow" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a>
                                  before posting!<br>
                                  &gt; <br>
                                  &gt; End of gmx-users Digest, Vol 91,
                                  Issue 36<br>
                                  &gt;
                                  *****************************************<br>
                                  <br>
                                  --<br>
                                  gmx-users mailing list    <a
                                    moz-do-not-send="true"
href="http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org"
                                    rel="nofollow" target="_blank">gmx-users@gromacs.org</a><br>
                                  <a moz-do-not-send="true"
                                    href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
                                    rel="nofollow" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
                                  Please search the archive at <a
                                    moz-do-not-send="true"
                                    href="http://www.gromacs.org/Support/Mailing_Lists/Search"
                                    rel="nofollow" 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
                                    moz-do-not-send="true"
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>
                                  Can't post? Read <a
                                    moz-do-not-send="true"
                                    href="http://www.gromacs.org/Support/Mailing_Lists"
                                    rel="nofollow" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
                                </div>
                              </blockquote>
                            </td>
                          </tr>
                        </tbody>
                      </table>
                      <br>
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                        class="yiv1828806674mimeAttachmentHeader"></fieldset>
                      <br>
                    </blockquote>
                    <br>
                  </div>
                </div>
                <br>
                -----下面为附件内容-----<br>
                <br>
                <div class="plainMail">-- <br>
                  gmx-users mailing list    <a moz-do-not-send="true"
href="http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org"
                    ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
                  <a moz-do-not-send="true"
                    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
                    moz-do-not-send="true"
                    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 moz-do-not-send="true"
href="http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org"
                    ymailto="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
                  Can't post? Read <a moz-do-not-send="true"
                    href="http://www.gromacs.org/Support/Mailing_Lists"
                    target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a></div>
              </blockquote>
            </td>
          </tr>
        </tbody>
      </table>
      <br>
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      <br>
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