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
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Dec 07 2018 - 00:00:03 PST
