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

[Seketoulie Keretsu]

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

[Benson Muite]

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:

https://docs.scipy.org/doc/numpy-1.10.1/user/install.html

Regards,

Benson

Post by Seketoulie Keretsu
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
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