[gmx-users] qmmm

[Adamu, Aliyu]

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-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Groenhof, Gerrit [ggroenh at gwdg.de]
Sent: Wednesday, November 2, 2016 8:03 AM
To: gromacs.org_gmx-users at 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.12 at aberdeen.ac.uk>
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Subject: Re: [gmx-users] qmmm
Message-ID:
        <AM4PR0101MB1956D3160A16D11B69CA74B2EFA10 at 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-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Groenhof, Gerrit [ggroenh at gwdg.de]
Sent: Tuesday, November 1, 2016 12:45 PM
To: gromacs.org_gmx-users at 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.12 at aberdeen.ac.uk>
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Subject: [gmx-users] qmmm
Message-ID:
        <AM4PR0101MB1956941D56C940378935BBB3EFA10 at 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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