[gmx-users] numpy related problem in GROMACS protein-ligand file preperation

Benson Muite benson.muite at ut.ee
Thu Dec 6 13:51:39 CET 2018

Hi Seketoulie,

If you have administrator rights on a CentOS system

sudo yum search numpy

will let you know what numpy versions have already been packaged.

You can also use

pip install --user numpy

or build from source:




On 12/6/18 1:57 PM, Seketoulie Keretsu wrote:
> Dear Experts,
> I am fairly new to gromacs (and linux CENTOS). I have recently
> installed the Gromacs18 successfully. However while doing the
> Protein-Lig tutorial I came across this problem while running the
> python script:
> Traceback (most recent call last):
>   File "cgenff_charmm2gmx.py", line 46, in <module>
>     import numpy as np
> ImportError: No module named numpy
> I have python 2.7.5 installed on my system. I am unable to find
> solutions related to this. Kindly advise how to correct this?  A hint
> on the possible cause will be awesome too.
> Note: I also have Amber18 installed on my the same system which
> apparently installs numpy.
> Thanking you.
> Sincerely,
> Seketoulie

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