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Just put something in QMMMscheme etc.. This will subsequently be
overwritten by whatever you have in your ORCA file.<br>
<br>
Micha<br>
On 07/11/11 12:54, xi zhao wrote:
<blockquote
cite="mid:1320670444.82465.YahooMailClassic@web15103.mail.cnb.yahoo.com"
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<div>All users:</div>
<div><br>
</div>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">According to <span style="COLOR: black"><a
moz-do-not-send="true"
href="http://wwwuser.gwdg.de/%7Eggroenh/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>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
style="COLOR: black" lang="EN-US"><font size="3"><font
face="Times New Roman">BASENAME=pyp_qm<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><font
size="3"><font face="Times New Roman"><span
style="COLOR: black" lang="EN-US">here is the
BASENAME</span><span lang="EN-US">.ORCAINFO<span
style="COLOR: black"> file:<o:p></o:p></span></span></font></font>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
style="COLOR: black" lang="EN-US"><font size="3"><font
face="Times New Roman">! RKS B3LYP/G SV(P)
TightSCF Opt<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><o:p><font face="Times New Roman"
size="3"> </font></o:p></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
style="COLOR: black" lang="EN-US"><font size="3"><font
face="Times New Roman">here is the md file:<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">integrator<span style="mso-spacerun: yes">
</span>= md<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">tinit<span style="mso-spacerun: yes">
</span>= 0<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">dt<span style="mso-spacerun: yes">
</span>= 0.001<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">nsteps<span style="mso-spacerun: yes">
</span>= 500<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">nstcomm<span style="mso-spacerun: yes">
</span>= 1<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">comm_grps<span style="mso-spacerun: yes">
</span>= system<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><o:p><font face="Times New Roman"
size="3"> </font></o:p></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">emtol<span style="mso-spacerun: yes">
</span>= 100.0<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">emstep<span style="mso-spacerun: yes">
</span>= 0.001<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">nstcgsteep<span style="mso-spacerun: yes">
</span>= 50<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><o:p><font face="Times New Roman"
size="3"> </font></o:p></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">nstxout<span style="mso-spacerun: yes">
</span>= 1<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">nstvout<span style="mso-spacerun: yes">
</span>= 1<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">nstfout<span style="mso-spacerun: yes">
</span>= 1<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">nstlog<span style="mso-spacerun: yes">
</span>= 1<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">nstenergy<span style="mso-spacerun: yes">
</span>= 1<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">nstxtcout<span style="mso-spacerun: yes">
</span>= 1<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">xtc_grps<span style="mso-spacerun: yes">
</span>= system<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">energygrps<span style="mso-spacerun: yes">
</span>= QMatoms rest_Protein SOL<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><o:p><font face="Times New Roman"
size="3"> </font></o:p></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">nstlist<span style="mso-spacerun: yes">
</span>= 10<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">ns_type<span style="mso-spacerun: yes">
</span>= grid<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">pbc<span style="mso-spacerun: yes">
</span>= xyz<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">rlist<span style="mso-spacerun: yes">
</span>= 1.0<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><o:p><font face="Times New Roman"
size="3"> </font></o:p></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">coulombtype<span style="mso-spacerun: yes">
</span>= cut-off<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">rcoulomb <span style="mso-spacerun: yes"> </span>=
1.4<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">epsilon_r<span style="mso-spacerun: yes">
</span>= 1<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">vdwtype<span style="mso-spacerun: yes">
</span>= Cut-off<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">rvdw<span style="mso-spacerun: yes">
</span>= 1.4<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><o:p><font face="Times New Roman"
size="3"> </font></o:p></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">tcoupl<span style="mso-spacerun: yes">
</span>= berendsen<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">tc-grps<span style="mso-spacerun: yes">
</span>= rest_Protein SOL QMatoms<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">tau_t<span style="mso-spacerun: yes">
</span>= 0.1 0.1 0 ; QM atoms are uncoupled<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">ref_t<span style="mso-spacerun: yes">
</span>= 300 300 300<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">Pcoupl<span style="mso-spacerun: yes">
</span>= Berendsen<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">pcoupltype<span style="mso-spacerun: yes">
</span>= isotropic<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">tau_p<span style="mso-spacerun: yes">
</span>= 1.0<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">compressibility<span style="mso-spacerun:
yes"> </span>= 4.5e-5<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">ref_p<span style="mso-spacerun: yes">
</span>= 1.0<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><o:p><font face="Times New Roman"
size="3"> </font></o:p></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">free_energy<span style="mso-spacerun: yes">
</span>= no<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">init_lambda<span style="mso-spacerun: yes">
</span>= 0<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font face="Times New Roman" size="3">delta_lambda<span
style="mso-spacerun: yes"> </span>= 0</font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">QMMM<span style="mso-spacerun: yes">
</span>= yes<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">QMMM-grps<span style="mso-spacerun: yes">
</span>= QMatoms<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">QMmethod<span style="mso-spacerun: yes">
</span>=<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">QMbasis<span style="mso-spacerun: yes">
</span>=<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">QMMMscheme<span style="mso-spacerun: yes">
</span>= normal<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">QMcharge<span style="mso-spacerun: yes">
</span>= -1<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">CASelectrons<span style="mso-spacerun: yes">
</span><span style="mso-spacerun: yes"> </span>=<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">CASorbitals<span style="mso-spacerun: yes">
</span>=<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">SH<span style="mso-spacerun: yes">
</span>=<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><o:p><font face="Times New Roman"
size="3"> </font></o:p></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">gen_vel<span style="mso-spacerun: yes">
</span>= no<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">gen_temp<span style="mso-spacerun: yes">
</span>= 300<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">gen_seed<span style="mso-spacerun: yes">
</span>= 173529<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><o:p><font face="Times New Roman"
size="3"> </font></o:p></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">constraints<span style="mso-spacerun: yes">
</span>= all-bonds<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">constraint_algorithm<span
style="mso-spacerun: yes"> </span>= LINCS<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">unconstrained_start<span
style="mso-spacerun: yes"> </span><span
style="mso-spacerun: yes"> </span>= yes<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">shake_tol<span style="mso-spacerun: yes">
</span>= 0.0001<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">lincs_order<span style="mso-spacerun: yes">
</span>= 4<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New
Roman">lincs_warnangle<span style="mso-spacerun:
yes"> </span>= 30<o:p></o:p></font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font face="Times New Roman" size="3">morse<span
style="mso-spacerun: yes"> </span>=
no</font></span>
</p>
<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>According
to the <span style="COLOR: black">instruction “</span>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, </font></font></span>
</p>
<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>But
When grompp</font></font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font face="Times New Roman" size="3">grompp_c
-f pyp.mdp -c pyp.gro -p pyp.top -n pyp.ndx -o
pyp_qm.tpr</font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font face="Times New Roman" size="3">……….</font></span>
</p>
<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>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font face="Times New Roman" size="3">Invalid
QMMM input: 1 groups 0 basissets and 0 methods.</font></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><o:p><font face="Times New Roman"
size="3"> </font></o:p></span>
</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font face="Times New Roman" size="3">How
to deal with it? Please help me!</font></span><br>
<br>
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