Re: [AMBER] numpy related problem in amber

From: Seketoulie Keretsu <>
Date: Fri, 7 Dec 2018 15:02:39 +0900

Dear David,

I have passed the command as you suggested and got the following outcome:
[biopo5.localhost ~]$ amber.python
Python 2.7.13 |Continuum Analytics, Inc.| (default, Dec 20 2016, 23:09:15)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
Anaconda is brought to you by Continuum Analytics.
Please check out: and
>>> import numpy
>>> 1+2
Looks like python is working fine. And as you speculated, there is
another version of python (default)
[biopo5.localhost protein_ligand]$ python
Python 2.7.5 (default, Oct 30 2018, 23:45:53)
[GCC 4.8.5 20150623 (Red Hat 4.8.5-36)] on linux2
Type "help", "copyright", "credits" or "license" for more information.

Also, "Yum info python" shows that the python version is 2.7.5. so I'm
guessing version 2.7.5 was installed before amber. Using "sudo Yum
remove python" to remove (2.7.5) is not working either.

As for the second question, "Can you say under what circumstances you
are getting this ImportError?
That is, what triggers it?"
Ans: I am running a python script to calculate CHARM topology for
gromacs (python JZ4 jz4_fix.mol2 jz4.str
charmm36-nov2018.ff) which requires the numpy and netwokX package
(networkx is already installed).
Seems like the problem in coming from the multiple python versions.
Kindly advise how to go about this.

I apologise this is not really a direct amber problem but I believe
someone who know about the working of ambers installations can solve.

Thank you. Seke
On Thu, Dec 6, 2018 at 11:02 PM David A Case <> wrote:
> On Thu, Dec 06, 2018, Seketoulie Keretsu wrote:
> >
> >I am not sure if the PATH are correctly added, please advise regarding
> >my PATH to add amber properly. Also numpy was supposed to be installed
> >(as per ./configure of amber) why do i still get the "ImportError: No
> >module named numpy". Please advise.
> Can you say under what circumstances you are getting this ImportError?
> That is, what triggers it?
> Did you accept the download of miniconda when you installed Amber?
> Try this:
> amber.python
> >>> import numpy
> If that works, then you are probably accessing some other python on your
> system, which is not the miniconda one the Amber installed. (just a
> guess: we would need to know answers to the questions above.)
> ...good luck...dac
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Received on Thu Dec 06 2018 - 22:00:02 PST
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