Re: [AMBER] QM/MM Interface

From: Dr. Andreas W. Goetz <>
Date: Mon, 23 May 2016 19:44:41 -0700

Dear Stano,

Thank you for helping to solve this problem.

As a follow-up, step 2) below should not be required. The qm/mm interface in Amber checks for the Orca installation path and uses the full path to call orca, so it should work in parallel.

All the best,

Dr. Andreas W. Goetz
Assistant Project Scientist
San Diego Supercomputer Center
Tel: +1-858-822-4771

> On May 21, 2016, at 12:37 AM, Stanislav Simko <> wrote:
> 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:
> 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
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Received on Mon May 23 2016 - 20:00:02 PDT
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