Command: python cgenff_charmm2gmx.py jz4 jz4_fix.mol2 jz4.str charmm-mar2019.ff
Error:
Traceback (most recent call last):
File "cgenff_charmm2gmx.py", line 47, in
import networkx as nx
File "/mnt/c/project/networkx/__init__.py", line 23
f"{release.authors['Hagberg'][0]} \n"
SyntaxError: invalid syntax
I am unable to understand what is the error in syntax here.
I have tried importing networkx . But i don't know if it is installed or not .I am using ubuntu on window. I downloaded python networkx 1.11 file but don't know how to install it into ubuntu.
You can install specific versions of python packages with the pip command like this:
pip install ==
In your case it would be:
pip install networkx==1.11
Also, make sure you're using Python version 2.7. This script is NOT compatible with Python 3.
Thank you Fotis Baltoumas .i have installed pythone three it worked. now i am getting new error .
File "cgenff_charmm2gmx_py3_nx2.py", line 991, in
if(float(nx.__version__) < 2.0):
ValueError: could not convert string to float: '2.5rc2.dev_20200823003249'
According to my understanding there is some problem with line 991 of the file but i am unable to identify that problem . This is line 991:
if(float(nx.__version__) < 2.0):
print("Your NetworkX version is: ",nx.__version__)
print("This script requires a version in the 2.x series")
print("Your NetworkX package is incompatible with this conversion script and cannot be used.")
Ok, this is new information: first of all, you're using some newer version of the script that works with python 3 and networkX 2.0 or newer (I wasn't even aware that this existed, by the way). NetworkX 1.11 will not help you there.
The error shown is that the script expects a real number (2.0, 2.1, 2.5 etc) as a version name, while the version name of your networkx package is a string ( 2.5rc2.dev_20200823003249).
You could try converting your script by changing the line:
if(float(nx.__version__) < 2.0):
to something like this:
if (float(nx.__version__[0:3])
Fotis Baltoumas i have python3 and networkx 2.5 and used this script which is for python3 and networkx2 .still above mentioned value error occured . i identified that this script is just for gromacs 2020 .i am using gromacs 5.1.1 . Now i am trying to find script that works for this version of gromacs. i also tried using:
python3 cgenff_charmm2gmx.py jz4 jz4_fix.mol2 jz4_clean.str charmm36-mar2019.ff
File "cgenff_charmm2gmx.py", line 58
print "--Version of CGenFF detected in ",str_filename,":",strver
^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print("--Version of CGenFF detected in ",str_filename,":",strver)?
i think this this script is for pythone 2 . last time i tried to install python2.7 by uninstalling python3 and everything was messed up .i had to uninstall ubuntu and reinstall everything.
Fotis Baltoumas Thank you for your help . this worked
if (float(nx.__version__[0:3])
- Badges
- Science topic
- Similar topics
- Filing