I think Koushik is right. I remember I forgot to source the bashrc. Thank
you for clarifying the issue!
On Wed, Jun 15, 2016 at 11:50 AM, Abdul-Rashid Iii Sampaco <
absampaco.up.edu.ph> wrote:
> 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
