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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Received on Tue Jun 14 2016 - 20:30:02 PDT
