From: <>
Date: Thu, 1 Mar 2018 11:23:16 +0800


My QM/MM calculations failed using amber/orca.
The prmtop and crd files come from the online tutorial
My workstations: 16 CPU, one GPU, single computer, openmpi
Here is the input file:
Initial min of our structure QMMM
  imin=1, maxcyc=500, ncyc=200,
  cut=8.0, ntb=1, ntc=2, ntf=2,

Here is the QM part in output file:
| !!!!!!!!!!!!!!!!!!!!!!!!! WARNING !!!!!!!!!!!!!!!!!!!!!!!!!!!!!
| Not all MPI implementations fully support system calls that execute
| MPI parallel programs. In this case it will not be possible to run
| MPI parallel versions of both sander and the external QM program.
| !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

| Please also cite the following work for the use of the QM/MM interface:

| A. W. G"otz, M. A. Clark, R. C. Walker
| "An extensible interface for ab initio QM/MM molecular dynamics simulations
| with AMBER"
| J. Comput. Chem. 35 (2014) 95-108.
| DOI: 10.1002/jcc.23444

 Constants for unit conversion taken from
 Mohr, Taylor, Newell, Rev. Mod. Phys. 80 (2008) 633-730
 and using the thermochemical calorie (1 cal = 4.184 J):

 A_TO_BOHRS = 1.889726132873E+00
 AU_TO_KCAL = 6.2750946943E+02
 AU_TO_DEBYE = 2.54174623E+00

>>> Running QM calculation with Orca <<<

 SANDER BOMB in subroutine get_namelist (qm2_extern_orc_module)
 The charge and spin keywords are deprecated
 Please specify charge (qmcharge) and spin multiplicity (spin) in the &qmmm namelist.

Here is the message in command line:
:~/orca/projects/NMA$ mpirun -np 8 sander.MPI -O -i -o min_qmmm.out -p NMA.prmtop -c NMA.inpcrd -r min_qmmm.rst
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.


How to solve this problem?
Looking forward to hear your help.

Yuan Min
From: Goetz, Andreas
Date: 2018-02-27 05:04
To: AMBER Mailing List
Subject: Re: [AMBER] AMBER/ORCA for QM/MM
The interface will work with Orca versions 3 (e.g. 3.0.3) and 4 (e.g. 4.0.2). See also previous messages on this mailing list
Link atoms work exactly as with the built-in semiempirical and DFTB methods. They will be added automatically if your QM/MM boundary crosses covalent bonds. Make sure to cut only across single bonds and not across polar bonds, i.e. C-C single bonds typically are appropriate. See also the Amber manual.
All the best,

Dr. Andreas W. Goetz
Assistant Research Scientist
San Diego Supercomputer Center
Tel: +1-858-822-4771
> On Feb 26, 2018, at 6:24 AM, wrote:
> Hi,
> I want to use AMBER/ORCA to achieve QM/MM calculations.
> Which version of ORCA program is supported by AMBER16?
> For tutorial I only find one in which boundaries of QM an MM atoms are not involved.
> How to deal with the QM-MM boundary if they are linked via covalent bonds?
> Looking forward to hear your reply.
> BestWishes,
> YuanMin
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Received on Wed Feb 28 2018 - 19:30:02 PST
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