[gmx-users] qmmm

[Adamu, Aliyu]

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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