Whatever it is, I hope it does not affect my future computations on amber.
Thank you so much!
Rashid
On Wed, Jun 15, 2016 at 11:26 AM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> 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.
> > > > > > > > _______________________________________________
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Received on Tue Jun 14 2016 - 21:00:03 PDT
