AMBER Archive (2009)

Subject: Re: [AMBER] Re: Fw: Help required in Amber10 Installation

From: Sudeep Narayan Banerjee (sudeep_at_bose.res.in)
Date: Thu Oct 15 2009 - 07:53:42 CDT

Dear Nicolas,

     The environment variables are defined as asked in the Amber10.pdf file.
I did the following steps:
1. Downloaded AmberTools & Amber10
2. extracted AmberTools first & then Amber10 under the same directory amber10/
3. Defined the variables as follows in .bashrc file (also tried with
.bash_profile)
set AMBERHOME=/root/amber10
PATH=$PATH:$AMBERHOME/exe
export AMBERHOME=/root/amber10/
4. did source .bashrc (or .bash_profile)
5. then i did echo $AMBERHOME, it gave me null. Whereas it should have shown
me the complete path"/root/amber10/"

Please guide accordingly. I am using Fedora 8.0 as root with bash shell.

Best Regards,
Sudeep Narayan Banerjee
Junior Computer Engineer
Email: sudeep_at_bose.res.in
S N Bose National Centre For Basic Sciences
Block JD, Sector III
Saltlake, Kolkata 700098

---------- Original Message -----------
From: Nicolas Sapay <nicolas.sapay_at_cermav.cnrs.fr>
To: AMBER Mailing List <amber_at_ambermd.org>
Cc: sudeep_at_bose.res.in
Sent: Thu, 15 Oct 2009 14:34:28 +0200
Subject: Re: [AMBER] Re: Fw: Help required in Amber10 Installation

> Hello,
>
> Did you source your .bashrc or .bash_profile after your
> modifications? If not, you have to:
>
> source .bashrc
>
> Cheers,
> Nicolas
>
> Sudeep Narayan Banerjee a écrit :
> > Dear All,
> >
> > I tried to define the environment variables in .bashrc file, opened a new
> > shell & typed in echo $AMBERHOME...it gave me nothing. I even tried with
> > .bash_profile file but still same output, that's nothing, null. In the
> > Amber10.pdf file its written that "You should then add $AMBERHOME/exe to your
> > PATH." I am defining the line in the same file .bashrc and once again i tried
> > with .bash_profile like
> >
> > set AMBERHOME=/root/amber10
> > PATH=$PATH:$AMBERHOME/exe
> > export AMBERHOME=/root/amber10/
> >
> > After that whenever I am doing cd $AMBERHOME/src it says "bash: cd: /src: No
> > such file or directory". What to do in this case? I am doing from root.
> > Kindly help!
> >
> > Can I install it in CentOS?
> >
> >
> >
> >
> > Best Regards,
> > Sudeep Narayan Banerjee
> > Junior Computer Engineer
> > Email: sudeep_at_bose.res.in
> > S N Bose National Centre For Basic Sciences
> > Block JD, Sector III
> > Saltlake, Kolkata 700098
> >
> >
> > ---------- Original Message -----------
> > From: Chris Whittleston <csw34_at_cam.ac.uk>
> > To: AMBER Mailing List <amber_at_ambermd.org>
> > Sent: Wed, 7 Oct 2009 18:48:18 +0100
> > Subject: Re: [AMBER] Re: Fw: Help required in Amber10 Installation
> >
> >
> >> David is right - you need to use a new shell because .bashrc is only
> >> read in
> >> (and the variables set) when you start a shell. If you want to re-
> >> read .bashrc manually, you can by typing:
> >>
> >> source .bashrc
> >>
> >> then try:
> >>
> >> echo $AMBERHOME
> >>
> >> Chris
> >>
> >> 2009/10/7 Bill Ross <ross_at_cgl.ucsf.edu>
> >>
> >>
> >>> In bash, if .bashrc doesn't work, you can try .profile
> >>>
> >>> export AMBERHOME=/some/dir/path
> >>>
> >>> Bill
> >>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER_at_ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>>
> >> --
> >> Chris Whittleston
> >> Department of Chemistry
> >> University of Cambridge
> >> Lensfield Road, Cambridge, CB2 1EW
> >> Email: csw34_at_cam.ac.uk
> >> Tel: +44 (0)1223 336423
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER_at_ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > ------- End of Original Message -------
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
------- End of Original Message -------

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