Re: [AMBER] AMBER/ORCA for QM/MM

From: <minyuan.mail.ustc.edu.cn>
Date: Thu, 1 Mar 2018 16:09:39 +0800

Hi, Andy

Thank you for your reply. It started to run after removing chagre in &orc namelist.
But it failed again.
**********************************************************************************************************
The orc_job.engrad file is empty, thus the corresponding message is:
   4. RESULTS
--------------------------------------------------------------------------------
 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.)

***************************************************************************************************************************
The orc_job.inp file is:
# Run using SANDER file-based interface for Orca
#
%pal nprocs 8 end
!blyp SVP verytightscf
%method
  grid 4
  finalgrid 6
end
%scf
  maxiter 100
end
%MaxCore 30000
! ENGRAD
! Angs NoUseSym
%pointcharges "ptchrg.xyz"
*xyzfile 0 1 inpfile.xyz

*************************************************************************************************************
It seems that orca doesn't work.

Looking forward to hear your help.

BestWishes,
Yuan Min


minyuan.mail.ustc.edu.cn
 
From: Goetz, Andreas
Date: 2018-03-01 12:10
To: AMBER Mailing List
Subject: Re: [AMBER] AMBER/ORCA for QM/MM
Charge and spin need to be specified only in the &qmmm namelist, see the error message:
 
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.
 
All the best,
Andy
 
Sent from my iPhone
 
On Feb 28, 2018, at 19:24, "minyuan.mail.ustc.edu.cn<mailto:minyuan.mail.ustc.edu.cn>" <minyuan.mail.ustc.edu.cn<mailto:minyuan.mail.ustc.edu.cn>> wrote:
 
Hi,
 
My QM/MM calculations failed using amber/orca.
The prmtop and crd files come from the online tutorial http://ambermd.org/tutorials/advanced/tutorial2/section3.htm.
*******************************************************************************************************************
My workstations: 16 CPU, one GPU, single computer, openmpi
*******************************************************************************************************************
Here is the input file:
Initial min of our structure QMMM
&cntrl
imin=1, maxcyc=500, ncyc=200,
cut=8.0, ntb=1, ntc=2, ntf=2,
ifqnt=1
/
&qmmm
qmmask=':1-2',
qmcharge=0,
spin=1,
qm_theory='EXTERN',
qmshake=1,
qm_ewald=0
/
&orc
method='blyp',
basis='svp',
charge=0
/
 
*****************************************************************************************************************************
Here is the QM part in output file:
3.1 QM CALCULATION INFO
--------------------------------------------------------------------------------
| !!!!!!!!!!!!!!!!!!!!!!!!! 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 min_qmmm.in -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.
 
BestWishes,
Yuan Min
 
 
minyuan.mail.ustc.edu.cn<mailto:minyuan.mail.ustc.edu.cn>
 
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 http://archive.ambermd.org/201707/0486.html
 
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,
Andy

Dr. Andreas W. Goetz
Assistant Research Scientist
San Diego Supercomputer Center
Tel: +1-858-822-4771
Email: agoetz.sdsc.edu<mailto:agoetz.sdsc.edu>
Web: www.awgoetz.de<http://www.awgoetz.de>
 
On Feb 26, 2018, at 6:24 AM, minyuan.mail.ustc.edu.cn<mailto:minyuan.mail.ustc.edu.cn> 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
 
 
minyuan.mail.ustc.edu.cn<mailto:minyuan.mail.ustc.edu.cn>
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Received on Thu Mar 01 2018 - 00:30:03 PST
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