great.
But I believe the mistake was from something else. Extra '/' does not
really matter.
Hai
On Tue, Jun 14, 2016 at 11:21 PM, Abdul-Rashid Iii Sampaco <
absampaco.up.edu.ph> wrote:
> Hi,
>
> It finally works! Thank you so much. My mistake was copying "source
> /home/absampaco/amber16//amber.sh" directly to the terminal. It has one
> extra '/'.
>
> On Wed, Jun 15, 2016 at 10:59 AM, Hai Nguyen <nhai.qn.gmail.com> wrote:
>
> > hi
> >
> > it's clearly that you successfully installed all Python packages in
> > $AMBERHOME/lib/python2.7/site-packages
> >
> > What did you mean about
> >
> > > It says it cannot find the file.
> >
> > *What is "it"?*
> >
> > Have you* source $AMBERHOME/amber.sh* (if you are using Bourne shell
> (sh))
> > or *source $AMBERHOME/amber.csh* (if you are using C shell) yet?
> >
> > Can you send your screen capture showing the failure?
> >
> > Hai
> >
> > On Tue, Jun 14, 2016 at 10:54 PM, Abdul-Rashid Iii Sampaco <
> > absampaco.up.edu.ph> wrote:
> >
> > > Here. I also included python2.7/site-packages/
> > >
> > > On Wed, Jun 15, 2016 at 10:48 AM, Hai Nguyen <nhai.qn.gmail.com>
> wrote:
> > >
> > > > Please see my reply below.
> > > >
> > > > On Tue, Jun 14, 2016 at 10:06 PM, Abdul-Rashid Iii Sampaco <
> > > > absampaco.up.edu.ph> wrote:
> > > >
> > > > > Thank you for all your responses.
> > > > >
> > > > > I tried Case's suggestion. I understand the command forces the
> > computer
> > > > to
> > > > > download Miniconda. However, it fails to connect. The error message
> > is:
> > > > >
> > > > > Connecting to repo.continuum.io (repo.continuum.io
> > > > )|54.225.73.227|:443...
> > > > > failed: Connection timed out
> > > > >
> > > > > I'm not sure if this is already a problem on my internet
> connection,
> > or
> > > > how
> > > > > my terminal connects to the internet. I opened the link manually on
> > the
> > > > > browser and downloaded the shell file. I then used ./configure
> > > > > --with-python /path/to/miniconda.sh but it cannot be run by the
> > > > terminal. I
> > > > > understand now that the shell file cannot be run on the terminal.
> Any
> > > > > suggestions on how to run it?
> > > > >
> > > > > Btw, I also tried Nguyen's suggestion, but it does not work. It
> says
> > it
> > > > > cannot find the file.
> > > > >
> > > > >
> > > > Can you send the output of this
> > > >
> > > > *ls $AMBERHOME/lib/*
> > > >
> > > >
> > > > > To Chagas, I don't know exactly what you mean by "Try to copy your
> > > > content
> > > > > and put it in the .profile file". Which content? I'm not an
> > experienced
> > > > > Linux user. I'm sorry if you have to be very specific on your
> > > > instructions
> > > > > to me.
> > > > >
> > > > > Sincerely,
> > > > >
> > > > > Rashid
> > > > >
> > > > > On Tue, Jun 14, 2016 at 10:25 PM, Hai Nguyen <nhai.qn.gmail.com>
> > > wrote:
> > > > >
> > > > > > Hi
> > > > > >
> > > > > > First, do you see any folder in
> > > > $AMBERHOME/lib/python*X.Y*/site-packages?
> > > > > > where "X.Y" can be *2.7, 3.4, 3.5* (you should expect to see
> > parmed,
> > > > > > sander, pytraj, ...)
> > > > > >
> > > > > > If yes, do this again in your terminal
> > > > > >
> > > > > > source /home/absampaco/amber16//amber.sh
> > > > > >
> > > > > > If nothing works, please try Case's suggestion.
> > > > > >
> > > > > > Hai
> > > > > >
> > > > > > On Tue, Jun 14, 2016 at 4:22 AM, Abdul-Rashid Iii Sampaco <
> > > > > > absampaco.up.edu.ph> wrote:
> > > > > >
> > > > > > > Hi,
> > > > > > >
> > > > > > > I am installing AmberTools16 on my laptop using Ubuntu BioLinux
> > on
> > > > VM.
> > > > > I
> > > > > > > followed all instructions on the guide. Based on what I see,
> > > > everything
> > > > > > > works perfectly well after make install. However, the 'make
> test'
> > > > gives
> > > > > > > this error message:
> > > > > > >
> > > > > > > Error: Could not import Amber Python modules! Probably your
> Amber
> > > > > Python
> > > > > > > environment was not set up correctly.
> > > > > > >
> > > > > > > I already added the test -f /home/absampaco/amber16//amber.sh
> &&
> > > > source
> > > > > > > /home/absampaco/amber16//amber.sh to my ~/.bash.rc before the
> > 'make
> > > > > > > install'.
> > > > > > >
> > > > > > > I would appreciate any help given.
> > > > > > > _______________________________________________
> > > > > > > AMBER mailing list
> > > > > > > AMBER.ambermd.org
> > > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > > >
> > > > > > _______________________________________________
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> > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > >
> > > > > _______________________________________________
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> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
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> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > >
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> > >
> > >
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> >
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Received on Tue Jun 14 2016 - 20:30:03 PDT
