As I remembered in fixing the amber/orca problem, you can just alias orca
into a full path command in the script or environment.
The other problem is sander still using old Grid formats and that will not
be accepted by current ORCA 6.1, I posted the fix here or you can just
change the argument into defgrid2 or 3.
http://archive.ambermd.org/202512/0028.html
James Kress via AMBER <amber.ambermd.org> 於 2026年5月27日週三 上午1:39寫道：
> You might want to try the ORCA forum since the problem seems to reside in
> ORCA.
>
>
> https://orcaforum.kofo.mpg.de/index.php?sid=89c1171e8020013cf5b3d7a1ea1a513a
>
>
> On Tue, May 26, 2026 at 5:13 AM Anders Frederiksen via AMBER <
> amber.ambermd.org> wrote:
>
> > Hi Clorice,
> >
> >
> > thank you very much for this input. I have tried to implement your path
> > definitions in my slurm script, however still to no avail. I have below
> > pasted the relevant part of my slurm script to start the simulation
> >
> >
> >
> > ml PDC/24.11
> > ml amber/24-cpeGNU-24.11-ambertools-24-amdgpu
> > ml openmpi/5.0.8
> > ml orca/6.1.1
> >
> > ORCA_PATH=/pdc/software/24.11/other/orca/6.1.1/
> > ORCARUN=/pdc/software/24.11/other/orca/6.1.1/orca
> > export PATH="/pdc/software/24.11/other/orca/6.1.1/orca:$PATH"
> >
> > srun $AMBERHOME/bin/sander.MPI -O -i colvar.mdin \
> > -o orc_test.mdout \
> > -p neutral.prmtop \
> > -c rewrapped.rst7 \
> > -r cont.rst7 \
> > -x orc_test.nc \
> >
> >
> > similarly, my orca template contains
> > %pal nprocs 10 end
> >
> >
> > which ORCA correctly catches
> >
> > ************************************************************
> > * Program running with 10 parallel MPI-processes *
> > * working on a common directory
> *
> > ************************************************************
> > Unfortunately, the simulation still crashes
> >
> > Calling Command: mpirun -np 10
> > /pdc/software/24.11/other/orca/6.1.0/orca_startup_mpi orc_job.int.tmp
> > orc_job
> > [file orca_tools/qcmsg.cpp, line 394]:
> > .... aborting the run
> >
> > The mpirun call is not something I have inserted anywhere, it seems to me
> > to happen on ambers part, though I am not sure if it is an issue that
> stems
> > from the way the program was compiled on the cluster or if there is
> another
> > underlying issue.
> >
> >
> > I will try and mail this thread to Andreas in the hopes that he has a
> > solution.
> >
> >
> > Best,
> >
> > Anders
> >
> >
> >
> > ________________________________
> > From: Clorice Reinhardt <Clorice.Reinhardt.uvm.edu>
> > Sent: Monday, May 25, 2026 11:54:21 PM
> > To: amber.ambermd.org; Anders Frederiksen
> > Subject: Re: [AMBER] bug when running QM/MM with orca as external program
> >
> > Hi Anders,
> >
> > I have not any problems with Amber/ORCA interface. I'm not sure why you
> > are calling ORCA in this way... Amber calls ORCA when it needs the forces
> > on the atoms at each time step, or to perform the minimization.
> >
> > Therefore, you only write the command to call AMBER not ORCA in your job
> > submission file. The original QM/MM interface paper has a nice flow chart
> > if your confused on the flow of information. Amber writes the input files
> > for orca at each minimization or time step, you do not need to do this
> for
> > it.
> >
> > For example, my slurm file looks like the following for QM/M I do (with
> > some information redacted 🙂 )
> >
> >
> > module load amber/24
> > echo $AMBERHOME
> >
> > module load gcc/13.3.0
> > module load openmpi/5.0.5
> > module load orca/6.0.1
> >
> > ## amber can't find orca unless you explicitly tell it where the paths
> > are. Probably could remedy this by passing the path while compiling, but
> I
> > didn't compile the version on the cluster and it works fine
> >
> > ORCA_PATH=YOURPATH
> > ORCARUN=YOURPATHTOEXECUTEABLE
> > export PATH="/gpfs1/sw/x86_64/rh7/pkgs/orca/6.0.0/orca:$PATH"
> >
> > top=my_parmtop
> >
> > $sander -O -i qmmm_md.in -o qmmm_md.out -p ${top}.prmtop -c
> > YOUR_RESTART.rst -r qmmm_md.rst -x qmmm_md.netcdf
> >
> > I read in an orca template file with into amber (contain these among
> > others):
> > %pal nprocs 24 end
> > %maxcore 3600
> >
> > Confirming it worked (looking at orc_job.dat which gets produced each
> time
> > orca is called and is the default name of the output file):
> > " ************************************************************
> > * Program running with 24 parallel MPI-processes *
> > * working on a common directory *
> > ************************************************************
> >
> >
> ------------------------------------------------------------------------------
> > ORCA STARTUP CALCULATIONS
> > -- RI-GTO INTEGRALS CHOSEN --
> >
> >
> ------------------------------------------------------------------------------
> > "
> >
> > Your happy to reach out to me if you have questions. I run a ton of QM/MM
> > and have dug into the source code and used the interface with Qchem,
> > Gaussian and ORCA without a hitch, but Andreas Goetz is who'd I reach out
> > if you have questions. He wrote the original paper on the interface, and
> > he's super nice.
> >
> > https://scholar.google.com/citations?user=PJusscIAAAAJ&hl=en
> >
> > Clorice
> > ________________________________
> > From: Anders Frederiksen via AMBER <amber.ambermd.org>
> > Sent: Monday, May 25, 2026 9:52 AM
> > To: amber.ambermd.org <amber.ambermd.org>
> > Subject: [AMBER] bug when running QM/MM with orca as external program
> >
> > Dear amber forum,
> >
> > I have in the last week been working with the QM/MM interface of the
> > amber programme and especially focussing with performing a QM/MM
> > simulation with orca as the external program.
> >
> > I have had great success running with orca as external program on small
> > test systems for short simulations with sander running on multiple
> > processors through MPI and orca running on single core through num
> > threads = 1.
> >
> > However, if I want to run any kind of multi processing the QM part of
> > the simulation crashes with the error
> >
> > ORCA finished by error termination in orca_util
> > Calling Command: mpirun -np 2
> > /pdc/software/24.11/other/orca/6.1.0/orca_util_mpi orc_job orca_hostfile
> > orc_job
> > [file orca_tools/qcmsg.cpp, line 394]:
> > .... aborting the run
> >
> > This in principle is not surprising if we take a quick look at the orca
> > documentation where it states:
> >
> > Do not start the ORCA driver with mpirun!
> >
> > I have tested and if I use ORCA the intended way, that is calling ORCA
> > with its full path followed by the input file it runs just fine on
> > multiple processors and therefore the fix for the amber call should be
> > quite simple: Remove the "mpirun -np #MPIprocessors" call when orca is
> > initiated.
> >
> > I should not that this should not be a version dependent thing for orca
> > as I have found documentation all the way back in ORCA 3 (i.e.
> > documentation from 2015), stating that starting ORCA with mpirun will
> > make it crash.
> >
> > I have tried to work around the issue by using a template file
> > (use_template =1) however sadly AMBER seems to read the nprocs flag and
> > will make ORCA run through mpirun, leading to the same error as if
> > initiated with AMBER input.
> >
> >
> > If anyone have found another workaround I am all ears, though I hope
> > this mail reaches a developer as the fix on paper should be rather
> > simple, though given my inexperience in development it could not be as
> > simple as I want it to be.
> >
> > Best,
> >
> > Anders Frederiksen
> > Postdoctoral researcher
> > KTH, department of Chemistry, Stockholm, Sweden.
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
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>
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Received on Tue May 26 2026 - 11:00:04 PDT
