Dear Gerrit,
I did as you suggested and realised it is orca related problem. thanks a lot
for you help. it really mean a lot to me.
many thanks
Aliyu Adamu
________________________________________
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Groenhof,
Gerrit [ggro...@gwdg.de]
Sent: Wednesday, November 2, 2016 8:03 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] qmmm
Looks more like an issue running orca than with gromacs and it seems that
you're trying to run orca with mpi, but don't have an mpirun in your path. Can
you run ORCA stand-alone with the input file generated with gromacs? If it is
orca related, please contact Orca crew.
Best,
Gerrit
Message: 4
Date: Tue, 1 Nov 2016 23:38:04 +0000
From: "Adamu, Aliyu" <aliyu.adamu...@aberdeen.ac.uk>
To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org>
Subject: Re: [gmx-users] qmmm
Message-ID:
<am4pr0101mb1956d3160a16d11b69ca74b2ef...@am4pr0101mb1956.eurprd01.prod.exchangelabs.com>
Content-Type: text/plain; charset="us-ascii"
Dear Gerrit,
thanks a lot for your email. when i used "export BASENAME=topol" as you
suggested, that particular error was solved. but yet i got another error
reading as:
starting mdrun 'Protein'
5000 steps, 5.0 ps.
Calling '/home/birg/orca//orca topol.inp >> topol.out'
sh: 1: mpirun: not found
ORCA finished by error termination in ORCA_GTOInt
Segmentation fault (core dumped)
I dont know what is wrong, because i am running the calculation on just one PC
many thanks
Aliyu Adamu
________________________________________
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Groenhof,
Gerrit [ggro...@gwdg.de]
Sent: Tuesday, November 1, 2016 12:45 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] qmmm
depending on the shell try using "export BASENAME=topol" or "setenv BASENAME
topop' instead. You can check if things worked by typing echo $BASENAME which
should be topol.
I am surprised you did not get an error message form the shell after typing
these lines...
Gerrit
Message: 3
Date: Tue, 1 Nov 2016 10:57:07 +0000
From: "Adamu, Aliyu" <aliyu.adamu...@aberdeen.ac.uk>
To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org>
Subject: [gmx-users] qmmm
Message-ID:
<am4pr0101mb1956941d56c940378935bbb3ef...@am4pr0101mb1956.eurprd01.prod.exchangelabs.com>
Content-Type: text/plain; charset="us-ascii"
Hello Justin
could you please help me out on how to get over this problem? I want to run
QM/MM calculation in GROMACS 4.6.7 and ORCA version 3.03. before i run the
mdrun command i set the environment variables: BASENAME and ORCA_PATH by typing
the following command in the shell:
BASENAME=topol
ORCA_PATH=/home/birg/orca
But when i type the command for the mdrun as:
mdrun -v -c qmmm1out.gro
it gives me error massage that reads as:
-------------------------------------------------------
Program mdrun, VERSION 4.6.7
Source code file: /home/birg/Downloads/gromacs-4.6.7/src/mdlib/qm_orca.c, line:
86
Fatal error:
$BASENAME not set
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
I dont know why is indicating basename not set. please help me out?
many thanks
Aliyu Adamu
------------------------------
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