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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:
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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 >> 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 moz-do-not-send="true" class="plink"
href="http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844"
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<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"><ucbtmbk@live.ucl.ac.uk></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"><ucbtmbk@live.ucl.ac.uk></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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<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"
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--- <b>11年11月7日,周一, Gerrit Groenhof <i><a
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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
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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 moz-do-not-send="true"
class="yiv1828806674moz-txt-link-abbreviated"
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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
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----------------------------------------------------------------------<br>
> <br>
> Message: 1<br>
> Date: Mon, 7 Nov 2011 20:54:04
+0800 (CST)<br>
> From: xi zhao <<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>><br>
> Subject: [gmx-users] orca and
qm/mm<br>
> 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>
> Message-ID:<br>
> <<a moz-do-not-send="true"
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> Content-Type: text/plain;
charset="utf-8"<br>
> <br>
> All users:<br>
> <br>
> <br>
> 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>
> 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>
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