Re: [AMBER] QM/MM Interface

From: Stanislav Simko <>
Date: Sat, 21 May 2016 09:37:58 +0200

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
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

to you orc_job.tpl file


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
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Received on Sat May 21 2016 - 01:00:04 PDT
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