Dear Xiangyu Jia,
This may be a bug in the code. TI with QM/MM using external QM programs has never been tested. I will have a look, which may take me a few days. In the meantime please follow Dave’s advise.
All the best,
Andy
—
Dr. Andreas W. Goetz
Assistant Project Scientist
San Diego Supercomputer Center
Tel: +1-858-822-4771
Email: agoetz.sdsc.edu
Web: www.awgoetz.de
> On Jun 27, 2016, at 5:07 AM, David A Case <david.case.rutgers.edu> wrote:
>
> On Mon, Jun 27, 2016, Xiangyu Jia wrote:
>>
>> Recently, Thermodynamic Integration method was used to calculate
>> the free energy difference between two states in my research.
>> Particularly, the Hamiltonians of both states were described by
>> QM/MM. However, the calculation stopped with the following error
>> message:
>>
>> "SANDER BOMB in subroutine check_installation
>> (qm2_extern_util_module). Internal error closing and deleting files with
>> path location of executable. Quitting now."
>>
>> So, does Sander.MPI support TI calculation for both states described
>> by QM/MM Hamiltonian ? Otherwise, how can I fix this problem ?
>
> Just to help the debugging:
>
> 1. Can you confirm that a standard (non-TI) calculation, with everything else
> the same, runs OK?
>
> 2. Please try a short TI run using one of the built-in QM Hamiltonians, such
> as PM6. Does this trigger any errors?
>
> ...dac
>
>
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Received on Mon Jun 27 2016 - 14:30:02 PDT
