Re: [AMBER] Fwd: Error during installation process

From: Danu Fajar <dfr879.gmail.com>
Date: Wed, 1 Feb 2017 10:28:45 +0700

1. First, extract the files:

*cd /home/danu/amber/amber16*

*tar -xvf AmberTools16.tar.bz2*


2. Next, set AMBERHOME environment variable:

*export AMBERHOME=/home/myname/amber16 (*I did this in

* sudo –H gedit /etc/environtment) *3. Next, install some compilers and
other libraries.
*sudo apt-get install csh flex gfortran g++ xorg-dev \*

*zlib1g-dev libbz2-dev patch python-tk python-matplotlib*

4. Now, in the AMBERHOME directory, I run the configure script:

*cd $AMBERHOME*

*./configure gnu*

It created two resource files in the AMBERHOME directory: amber.sh and
amber.csh.

5. set up shell environment for Amber:



*source /home/danu/amber/amber16/amber.sh *

6. Then,

*make install *(but if I didn’t use *sudo*, the permission is always
denied, so I use *sudo make install)*

that was the last steps before the error happen
the error is show in the attachment

I'm sorry if I didn't give every information you need to help me, just like
I said before, I'm a newbie in linux machine, so please be patient helping
me. Just tell me if I didn't give the correct information you need to help
me.

On Wed, Feb 1, 2017 at 12:58 AM, Hai Nguyen <nhai.qn.gmail.com> wrote:

> Please attach the output of everything you did in this email.
>
> (including running ./configure, make install ,...)
>
> Also include output of the permission denied.
>
> Hai
>
> On Tue, Jan 31, 2017 at 12:37 PM, Danu Fajar <dfr879.gmail.com> wrote:
>
> > hello HAI, I don't know, I just followed the manual from the begining
> since
> > I'm a newbie.
> > if I didn't use sudo, the permission is always denied.
> > can u give me some helpful suggestion or tell me the way you did for your
> > installation please.
> >
> > On Tue, Jan 31, 2017 at 9:29 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> >
> > > hi
> > >
> > > which compiler you are using?
> > >
> > > lease do NOT use sudo.
> > >
> > > Hai
> > >
> > > On Tue, Jan 31, 2017 at 9:25 AM, Danu Fajar <dfr879.gmail.com> wrote:
> > >
> > > > Dear AMBER expert,
> > > >
> > > > I've followed the instruction in http://ambermd.org/doc12/Amber
> 16.pdf
> > > > but in the installation process (page 25 point 5 or page 26 point 6),
> > > > there's an error when "make install" (attachment number 2) and also I
> > > can't
> > > > identify the problem event I've follow point 7.it also has an error
> > > > (attachment number 3) and it says I haven't set the source. In Fact,
> > I've
> > > > done that first (attachment number1) before "make install". How can I
> > fix
> > > > it?
> > > >
> > > > Sincerely,
> > > > Danu Fajar
> > > >
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > >
> > > _______________________________________________
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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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>


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Received on Tue Jan 31 2017 - 19:30:03 PST
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