Hi Andy,
Set num_threads to either 1 or 8, fullpath/orca inputfile.inp > output.out, seccessfully completed.
The orca runs only using the full path, thougth I have added its path in ~/.bashrc.
If using command: orca inputfile.inp > output.out, message comes as,
/usr/lib/python3/dist-packages/pyatspi/__init__.py:17: PyGIWarning: Atspi was imported without specifying a version first. Use gi.require_version('Atspi', '2.0') before import to ensure that the right version gets loaded.
from gi.repository import Atspi
I'M confused.
BestWishes,
Yuan Min
minyuan.mail.ustc.edu.cn
From: Goetz, Andreas
Date: 2018-03-01 16:25
To: AMBER Mailing List
Subject: Re: [AMBER] AMBER/ORCA for QM/MM
You are not giving us enough information to debug your problem. Have a look at the Orca output file. This should give you more information on what went wrong. Also, it is a good idea to first make sure that everything works as expected with the serial version.
All the best,
Andy
—
Dr. Andreas W. Goetz
Assistant Research Scientist
San Diego Supercomputer Center
Tel: +1-858-822-4771
Email: agoetz.sdsc.edu
Web: www.awgoetz.de
> On Mar 1, 2018, at 12:09 AM, minyuan.mail.ustc.edu.cn wrote:
>
> 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 - 02:00:02 PST
