Hi Collin,
i just tried to run your orca input with one of mine setups and it
works well. When running directly by orca, do you get as output only a
few files - .pcgrad, .gbw, .prop and most importantly .engrad that is
not zero, or a lot of other files? (Lot of other files named orc_job*
suggests that orca crashed). Also, what is the case for the actual run
in Amber? If you get a lot of files, or you do not get .engrad file
than it means that orca crashed or did not run at all respectively.
From your error message i can only know that .engrad file is either
zero or not existing.
Regards,
stano.
On Sat, 2016-05-21 at 23:00 +0000, Nisler, Collin R. wrote:
> Hi Stano, thanks very much for the thorough response. I have tried
> your suggestions, but I'm getting the same response unfortunately.
> When I try typing
>
> orca orc_job.inp
>
> on the command line (with orc_job.inp being the input file presumably
> generated by sander) orca runs fine, which is puzzling. If sander
> runs orca by calling "orca orc_job.inp" then it doesn't make sense
> this wouldn't work, since it works when doing it "by hand". This is
> the orc_job.inp file generated:
>
> # ORCA input file for BLYP/SVP simulation
> ! BLYP SVP
> ! SlowConv
>
> %basis
> GTOAux = AutoBuild
> end
>
> %scf
> MaxIter 400
>
> DIISMaxEq 15
> directresetfreq 13
>
> end
> ! ENGRAD
> ! Angs NoUseSym
> %pointcharges "ptchrg.xyz"
> *xyzfile -2 1 inpfile.xyz
>
> Again, thanks for your time.
>
> Collin
>
> ________________________________________
> From: Stanislav Simko <s.simko.uu.nl>
> Sent: Saturday, May 21, 2016 2:37:58 AM
> To: amber.ambermd.org
> Subject: Re: [AMBER] QM/MM Interface
>
> Dear Collin,
> I've just been dealing with similar problems and for me there are
> several reasons for this:
> 1) there's already another program installed that is called orca
> (screen reader). In this case you just need to do "prepend-path" to
> your orca location, i.e. either (for bash):
> prepend-path PATH "/path/to/orca"
> or smth. like:
> export PATH=path/to/orca:$PATH
>
> 2) Assume that it's installed in the "/apps/orca_directory"
> directory.
> When running ORCA in parallel you MUST specify whole path to orca
> binary file, i.e.:
> /apps/orca_directory/orca input > output
>
> however, I think this is not the case for the Amber that runs it just
> like "orca" command. Therefore, I suggest you to :
>
> a) create alias for orca command in your .bashrc file, or somewhere
> else:
> alias orca='/full/path/to/orca_dir/orca'
>
> b) add following lines to your submit script so that the alias gets
> interpreted (bash terminal):
> . ~/bashrc
> shopt -s expand_aliases
>
> 3) It may also be that you Orca calculation does not reach the point
> where it creates .engrad file. To test for that I suggest you to just
> take the .inp + coordinates + charges prepared by the Amber and run
> it
> directly by Orca to find out. It is very probable that you need to
> add
> section:
> %BASIS GTOAUX=AutoBuild END
>
> to you orc_job.tpl file
>
> Regards,
> stano.
>
>
>
>
>
> On Sat, 2016-05-21 at 05:37 +0000, Nisler, Collin R. wrote:
> >
> > Hello, I am attempting to run a QM/MM simulation with an external
> > interface to Orca. I am able to run it on my machine (albeit very,
> > very slowly). I get the Orca output files and the SCF converges
> > well.
> > However, when I try to run this in parallel (on a supercomputer) I
> > am
> > getting the following error:
> >
> >
> > SANDER BOMB in subroutine read_results (qm2_extern_orc_module)
> > Error reading Orca output from file orc_job.engrad
> > (Current total energy or gradient not found or unsupported units.)
> >
> > I get a similar response when I try to use qchem with amber. I
> > think
> > Amber and Orca are just not able to communicate like they should,
> > but
> > I am completely unsure as to why. This happens both when I submit
> > the
> > job in a batch script, or on the command line. Any suggestions
> > would
> > be greatly appreciated, thanks for your time.
> >
> > Collin Nisler
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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--
Stanislav Simko.
PhD applicant
Inorganic Chemistry and Catalysis
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Received on Sat May 21 2016 - 17:00:05 PDT
