[gmx-users] gromacs.org_gmx-users Digest, Vol 140, Issue 38

[Puneet]

Hii Peter

Thank you for your valuable suggestion. I will check and ask you again
whether it is working or not.

Regards
Puneet

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Sent: 10 December 2015 16:30
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Subject: gromacs.org_gmx-users Digest, Vol 140, Issue 38

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Today's Topics:

   1. Re: bash: genrestr: command not found (Peter Stern)


----------------------------------------------------------------------

Message: 1
Date: Thu, 10 Dec 2015 10:02:37 +0000
From: Peter Stern <peter.stern at weizmann.ac.il>
To: "'gmx-users at gromacs.org'" <gmx-users at gromacs.org>
Subject: Re: [gmx-users] bash: genrestr: command not found
Message-ID: <9B479B1E75CB414487F6812A62434B24B4784190 at IBWMBX04>
Content-Type: text/plain; charset="us-ascii"

This is a unix/linux problem, not a gromacs problem.
And as such, I strongly suggest that you not run such commands as root, but
rather as an ordinary user.
Running commands as root, especially if you know little or no unix/linux can
be very dangerous.
The problem is probably in your path.  The shell needs to know where the gmx
executable is located.
There are several linux approaches to that, but for now, find out where gmx
is installed, and do the following:
export GMXDIR="location of gmx executable"
source $GMXDIR/GMXRC 

Then it should work.

Regards,
Peter Stern

-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
[mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of
Puneet
Sent: Thursday, December 10, 2015 11:17 AM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] bash: genrestr: command not found

Hello 

 


I am using command 


"genrestr -f jz4.gro -o posre_jz4.itp -fc 1000 1000 1000" for Restraining
the Ligand but I am facing following error


[root at localhost AD]# gmx genrestr -f lig.gro -o lig.itp -fc 1000 1000 1000

bash: gmx: command not found

[root at localhost AD]#  genrestr -f lig.gro -o lig.itp -fc 1000 1000 1000

bash: genrestr: command not found

 

Kindly tell me where is the problem. Please reply me as soon as possible.

 

Thanks in advance

Puneet

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