Molecular Dynamics of Protein - Ligand complex on Gromacs Part-2 Ligand Topology 

I tried this: python3 cgenff_charmm2gmx_py3_nx2.py JZ4 ligand_fix.mol2 ligand_fix.str charmm36-jul2021.ff it gave the following error ImportError: cannot import name 'gcd' from 'fractions' (/usr/lib/python3.10/fractions.py), kindly help me

sir if my ligand have param penalty= 280.000 ; charge penalty= 218.103, u have recommend to solve this issue? Previously I had looked for a solution to this but had not found it

how to perform the ligand topology if it contains ions and heme?

Thank you for the great video

How to create a topology for a ligand that contains a metal atom? I need it for gromos 56A ff.

Sir, what should I do, the penalty score of my ligand is 200

Found 43 atoms in the molecule, with 47 bonds. I get this after I run perl. Is this okay or does something need to be changed?

I'm getting the following error when I try to convert the pdb file of my ligand (this is the ligand I designed for my research) into the mol2 file: *** Open Babel Warning in PerceiveBondOrders Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders Do you have any suggestion to figure out this error?

How do you add the additional parameters to the forcefield? when I continue to energy min I have errors with processing my .itp files

If penalty is high then what should we do?

How to validate or optimization of param penalty of ligand my ligand param penalty has more than 200 how should I do optimization

Thank you very much for your time and effort.👋👋👋 In the step of preparing the topology of the Ligand, in particular during the generation of the .str file (stream" file). I tried with a complex based on Iron II (organo-mitalic compound) but an error that blocks me, because element (iron) not supported. Could you suggest me another method or another WEB server.

Hi, Thank u amazing explanation . can u tell me how solve, when adding ions step, error 1( file lig.itp, line 20): atomtype NPYD not found... im in a trouble in my research. This cant be solve to me😢

How can we generate ligand topology for a hybrid compound?

I am receiving this error after submitting to cgenff resonance warning: unfulfilled valence in aromatic subgraph; skipped molecule

Hello Sir. First of all thankyou for this tutorial ❤. I am facing issues with the numpy ..when I run the command it says “No Module named numpy”. can u please help me out in this. Thankyou

What if the force field is other than CHARMM36?

Hi sir, thank you for this tutorial it me showed me file not found error: no such file or directory jz4.str. How to fix this error

Which numpy version is required?

Why did you change 167 to 1?

I am not able to download .py file for charmm force field. How can i get it?

I'm unable to resolve this issue, please help me Traceback (most recent call last): File "/home/neel/Desktop/ras/4fyq/new md/cgenff_charmm2gmx_py3_nx2.py", line 54, in import networkx as nx File "/home/neel/miniconda3/lib/python3.9/site-packages/networkx/__init__.py", line 114, in import networkx.generators File "/home/neel/miniconda3/lib/python3.9/site-packages/networkx/generators/__init__.py", line 14, in from networkx.generators.intersection import * File "/home/neel/miniconda3/lib/python3.9/site-packages/networkx/generators/intersection.py", line 13, in from networkx.algorithms import bipartite File "/home/neel/miniconda3/lib/python3.9/site-packages/networkx/algorithms/__init__.py", line 16, in from networkx.algorithms.dag import * File "/home/neel/miniconda3/lib/python3.9/site-packages/networkx/algorithms/dag.py", line 23, in from fractions import gcd ImportError: cannot import name 'gcd' from 'fractions' (/home/neel/miniconda3/lib/python3.9/fractions.py)

Hi sir ;First of all thank you for this tutorial ; in the step of preparing the topology of the Ligand, After running this step Traceback (most recent call last): File "/home/cli/Bureau/MD/cgenff_charmm2gmx_py3_nx2.py", line 991, in if(float(nx.__version__) < 2.0): ValueError: could not convert string to float: '3.2.1' Could you please suggest anything to solve the problem?

I have a problem: cannot import name 'gcd' from 'fractions' (/usr/lib/python3.10/fractions.py). Thanks

Hi sir, thank you for your excellent tutorial. As followed by your instruction. After running this step: It showed some tracebacks and import error: cannot import 'gcd' from 'fraction' (/usr/lib/python3.10/fractions.py). Can you suggest me some steps to fix this error?

When I am doing this, facing a problem like that: ImportError: cannot import name 'gcd' from ' fractions' (/usr/lib/python3.10/fractions.py) Could you please suggest anything to solve the problem?