Conversion of .str file fails

User discussions
1

GROMACS version:
GROMACS modification: No

I am trying to convert the .str file using python script. I have created a separate conda environment with appropriate version of numpy and networkx (1.11). My command and the output are as below.

(charmm) md> python cgenff_charmm2gmx.py FUCOIDAN ligand_fix.mol2 ligand_fix.str charmm36-jul2021.ff


NOTE 1: Code tested with Python 3.5.2 and 3.7.3. Your version: 3.5.5 | packaged by conda-forge | (default, Jul 24 2018, 01:52:17) [MSC v.1900 64 bit (AMD64)]

NOTE 2: Code tested with NetworkX 2.3. Your version: 1.11

NOTE 3: Please be sure to use the same version of CGenFF in your simulations that was used during parameter generation:
--Version of CGenFF detected in  ligand_fix.str : 4.6
--Version of CGenFF detected in  charmm36-jul2021.ff/forcefield.doc : 4.6

NOTE 4: To avoid duplicated parameters, do NOT select the 'Include parameters that are already in CGenFF' option when uploading a molecule into CGenFF.
Traceback (most recent call last):
  File "cgenff_charmm2gmx.py", line 1041, in <module>
    m.read_charmm_rtp(rtplines,atomtypes)
  File "cgenff_charmm2gmx.py", line 600, in read_charmm_rtp
    nx.set_node_attributes(self.G, nodd)
TypeError: set_node_attributes() missing 1 required positional argument: 'values'
2

You’re using a version of the script that requires a newer NetworkX version. Download the appropriate script that matches your environment, or reconfigure the environment to use what the script requires.

3

Ohh. That is what it means. Thanks a ton! I would have blown another few hours studying networkx intestines.