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<P style="TEXT-INDENT: 10.5pt; MARGIN: 0cm 0cm 0pt; mso-char-indent-count: 1.0" class=MsoNormal><SPAN lang=EN-US><FONT size=3><FONT face="Times New Roman">According to <SPAN style="COLOR: black"><A href="http://wwwuser.gwdg.de/~ggroenh/qmmm.html#code" target=_blank><FONT color=#800080>http://wwwuser.gwdg.de/~ggroenh/qmmm.html#code</FONT></A>, I want to build qm/mm calculation by using gromacs <?xml:namespace prefix = st1 ns = "urn:schemas-microsoft-com:office:smarttags" /><st1:chsdate w:st="on" IsROCDate="False" IsLunarDate="False" Day="30" Month="12" Year="1899">4.5.3</st1:chsdate> + orca 2.8.0. I set up the BASENAME, ORCA_PATH and <SPAN style="mso-spacerun: yes"> </SPAN></SPAN>BASENAME.ORCAINFO <SPAN style="COLOR: black">as told in the instruction. <?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" /><o:p></o:p></SPAN></FONT></FONT></SPAN></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><FONT size=3><FONT face="Times New Roman"><B style="mso-bidi-font-weight: normal"><SPAN lang=EN-US>When</SPAN></B><SPAN lang=EN-US> BASENAME.ORCAINFO has no coordinates of QMatoms, the mdrun showns "<o:p></o:p></SPAN></FONT></FONT></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3><FONT face="Times New Roman">Back Off! I just backed up md.log to ./#md.log.1#<o:p></o:p></FONT></FONT></SPAN></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3><FONT face="Times New Roman">Getting Loaded...<o:p></o:p></FONT></FONT></SPAN></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><FONT size=3><FONT face="Times New Roman"><st1:City w:st="on"><st1:place w:st="on"><SPAN lang=EN-US>Reading</SPAN></st1:place></st1:City><SPAN lang=EN-US> file pyp_qm.tpr, VERSION <st1:chsdate w:st="on" IsROCDate="False" IsLunarDate="False" Day="30" Month="12" Year="1899">4.5.3</st1:chsdate> (double precision)<o:p></o:p></SPAN></FONT></FONT></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3><FONT face="Times New Roman">Loaded with Money<o:p></o:p></FONT></FONT></SPAN></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3><FONT face="Times New Roman">QM/MM calculation requested.<o:p></o:p></FONT></FONT></SPAN></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3><FONT face="Times New Roman">there we go!<o:p></o:p></FONT></FONT></SPAN></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3><FONT face="Times New Roman">Layer 0<o:p></o:p></FONT></FONT></SPAN></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3><FONT face="Times New Roman">nr of QM atoms 22<o:p></o:p></FONT></FONT></SPAN></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3><FONT face="Times New Roman">QMlevel: RHF/3<st1:chmetcnv w:st="on" TCSC="0" NumberType="1" Negative="True" HasSpace="False" SourceValue="21" UnitName="g">-21G</st1:chmetcnv><o:p></o:p></FONT></FONT></SPAN></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3><FONT face="Times New Roman">/home/user/orca_x86_64_exe_r2131/home/user/orca_x86_64_exe_r2131...<o:p></o:p></FONT></FONT></SPAN></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3><FONT face="Times New Roman">orca initialised...<o:p></o:p></FONT></FONT></SPAN></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3><FONT face="Times New Roman">Back Off! I just backed up ener.edr to ./#ener.edr.1#<o:p></o:p></FONT></FONT></SPAN></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3><FONT face="Times New Roman">starting mdrun 'PHOTOACTIVE YELLOW PROTEIN in water'<o:p></o:p></FONT></FONT></SPAN></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3><FONT face="Times New Roman">500 steps,<SPAN style="mso-spacerun: yes"> </SPAN>0.5 ps.<o:p></o:p></FONT></FONT></SPAN></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3><FONT face="Times New Roman">Calling '/home/user/orca_x86_64_exe_r2131/orca pyp_qm.inp >> pyp_qm.out'<o:p></o:p></FONT></FONT></SPAN></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3 face="Times New Roman"><STRONG>No atoms to convert in Cartesian2Internal" </STRONG></FONT></SPAN></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3><FONT face="Times New Roman">………<o:p></o:p></FONT></FONT></SPAN></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><FONT size=3><FONT face="Times New Roman"><B style="mso-bidi-font-weight: normal"><SPAN lang=EN-US>When</SPAN></B><SPAN lang=EN-US> BASENAME.ORCAINFO has coordinates of QMatoms, such as " <o:p></o:p></SPAN></FONT></FONT></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3><FONT face="Times New Roman">!RKS BP RI SV(P) SV/J TightSCF Opt<o:p></o:p></FONT></FONT></SPAN></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3><FONT face="Times New Roman">* xyz -1 2<o:p></o:p></FONT></FONT></SPAN></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3><FONT face="Times New Roman">O 29.8300000<SPAN style="mso-spacerun: yes"> </SPAN>35.2700000<SPAN style="mso-spacerun: yes"> </SPAN>32.7900000<o:p></o:p></FONT></FONT></SPAN></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3><FONT face="Times New Roman">H 30.0700000<SPAN style="mso-spacerun: yes"> </SPAN>34.9700000<SPAN style="mso-spacerun: yes"> </SPAN>34.6300000<o:p></o:p></FONT></FONT></SPAN></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3><FONT face="Times New Roman">C 31.5600000<SPAN style="mso-spacerun: yes"> </SPAN>34.7800000<SPAN style="mso-spacerun: yes"> </SPAN>32.3000000<o:p></o:p></FONT></FONT></SPAN></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3><FONT face="Times New Roman">LA 31.7400000<SPAN style="mso-spacerun: yes"> </SPAN>34.8400000<SPAN style="mso-spacerun: yes"> </SPAN>30.8800000<o:p></o:p></FONT></FONT></SPAN></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3><FONT face="Times New Roman">.......<o:p></o:p></FONT></FONT></SPAN></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3><FONT face="Times New Roman">mdrun shows :Back Off! I just backed up md.log to ./#md.log.1#<o:p></o:p></FONT></FONT></SPAN></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3><FONT face="Times New Roman">Getting Loaded...<o:p></o:p></FONT></FONT></SPAN></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><FONT size=3><FONT face="Times New Roman"><st1:City w:st="on"><st1:place w:st="on"><SPAN lang=EN-US>Reading</SPAN></st1:place></st1:City><SPAN lang=EN-US> file pyp_qm.tpr, VERSION <st1:chsdate w:st="on" IsROCDate="False" IsLunarDate="False" Day="30" Month="12" Year="1899">4.5.3</st1:chsdate> (double precision)<o:p></o:p></SPAN></FONT></FONT></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3><FONT face="Times New Roman">Loaded with Money<o:p></o:p></FONT></FONT></SPAN></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3><FONT face="Times New Roman">QM/MM calculation requested.<o:p></o:p></FONT></FONT></SPAN></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3><FONT face="Times New Roman">there we go!<o:p></o:p></FONT></FONT></SPAN></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3><FONT face="Times New Roman">Layer 0<o:p></o:p></FONT></FONT></SPAN></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3><FONT face="Times New Roman">nr of QM atoms 22<o:p></o:p></FONT></FONT></SPAN></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3><FONT face="Times New Roman">QMlevel: RHF/3<st1:chmetcnv w:st="on" TCSC="0" NumberType="1" Negative="True" HasSpace="False" SourceValue="21" UnitName="g">-21G</st1:chmetcnv><o:p></o:p></FONT></FONT></SPAN></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3><FONT face="Times New Roman">/home/user/orca_x86_64_exe_r2131/home/user/orca_x86_64_exe_r2131...<o:p></o:p></FONT></FONT></SPAN></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3><FONT face="Times New Roman">orca initialised...<o:p></o:p></FONT></FONT></SPAN></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3><FONT face="Times New Roman">Back Off! I just backed up traj.trr to ./#traj.trr.1#<o:p></o:p></FONT></FONT></SPAN></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3><FONT face="Times New Roman">Back Off! I just backed up traj.xtc to ./#traj.xtc.1#<o:p></o:p></FONT></FONT></SPAN></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3><FONT face="Times New Roman">Back Off! I just backed up ener.edr to ./#ener.edr.1#<o:p></o:p></FONT></FONT></SPAN></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3><FONT face="Times New Roman">starting mdrun 'PHOTOACTIVE YELLOW PROTEIN in water'<o:p></o:p></FONT></FONT></SPAN></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3><FONT face="Times New Roman">500 steps,<SPAN style="mso-spacerun: yes"> </SPAN>0.5 ps.<o:p></o:p></FONT></FONT></SPAN></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3><FONT face="Times New Roman">Calling '/home/user/orca_x86_64_exe_r2131/orca pyp_qm.inp >> pyp_qm.out'<o:p></o:p></FONT></FONT></SPAN></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3><FONT face="Times New Roman"><SPAN style="mso-spacerun: yes"> </SPAN>Unless this is specifically allowed this means that the basis set is not <o:p></o:p></FONT></FONT></SPAN></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3><FONT face="Times New Roman"><SPAN style="mso-spacerun: yes"> </SPAN>available for this element - Aborting the run<o:p></o:p></FONT></FONT></SPAN></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3><FONT face="Times New Roman">-------------------------------------------------------<o:p></o:p></FONT></FONT></SPAN></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3><FONT face="Times New Roman">Program mdrun_p, VERSION <st1:chsdate w:st="on" IsROCDate="False" IsLunarDate="False" Day="30" Month="12" Year="1899">4.5.3</st1:chsdate><o:p></o:p></FONT></FONT></SPAN></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3><FONT face="Times New Roman">Source code file: qm_orca.c, line: 409<o:p></o:p></FONT></FONT></SPAN></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3><FONT face="Times New Roman">Fatal error:<o:p></o:p></FONT></FONT></SPAN></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3><FONT face="Times New Roman">Call to '/home/user/orca_x86_64_exe_r2131/orca pyp_qm<o:p></o:p></FONT></FONT></SPAN></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3><FONT face="Times New Roman"><SPAN style="mso-spacerun: yes"> </SPAN><o:p></o:p></FONT></FONT></SPAN></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3><FONT face="Times New Roman">how to write the BASENAME.ORCAINFO?<o:p></o:p></FONT></FONT></SPAN></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3 face="Times New Roman">how to deal with LA in the gromacs for ORCA calculation?</FONT></SPAN></DIV><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></td></tr></table>