For me this is resolved by simply : sudo yum install numpy
basically this solves it but now i have multiple numpy and python in my system
On Fri, Dec 7, 2018 at 4:30 PM Hai Nguyen <nhai.qn.gmail.com> wrote:
>
> Please try
>
> amber.python cgenff_charmm2gmx.py
>
> Hai
>
> On Fri, Dec 7, 2018 at 12:47 AM Seketoulie Keretsu <sekekeretsu.gmail.com>
> wrote:
>
> > 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: http://continuum.io/thanks and https://anaconda.org
> > >>> import numpy
> > >>> 1+2
> > 3
> > >>>
> > 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 cgenff_charmm2gmx.py 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 <david.case.rutgers.edu>
> > 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 Fri Dec 07 2018 - 03:00:02 PST
