Molecular Dynamics of Protein - Ligand complex on Gromacs Part-2 Ligand Topology
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- เผยแพร่เมื่อ 11 ก.ย. 2024
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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
Try python version 3.5.2 or 3.7.3, also check networkx is 2.3.
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
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 to perform the ligand topology if it contains ions and heme?
How do you add the additional parameters to the forcefield? when I continue to energy min I have errors with processing my .itp files
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?
How to create a topology for a ligand that contains a metal atom? I need it for gromos 56A ff.
Thank you for the great video
Sir, what should I do, the penalty score of my ligand is 200
If penalty is high then what should we do?
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.
I am not able to download .py file for charmm force field. How can i get it?
Pls try again you should be able to do it
I am receiving this error after submitting to cgenff
resonance warning: unfulfilled valence in aromatic subgraph; skipped molecule
Your molecule should have explicit hydrogen atoms before submitting to cgenff server 👍
How to validate or optimization of param penalty of ligand my ligand param penalty has more than 200 how should I do optimization
How can we generate ligand topology for a hybrid compound?
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
Please check jz4.str file is persent in Gromacs working folder. And check weather you are "cd" into Gromacs working folder. 👍
@@pymolbiomolecules
Thank you sir for your quick reply
I've completed doing the md run successfully just now
Waiting for your 11th video sir
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😢
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
Yes, you have to install the numpy. To install give the command pip install numpy. Better alternative will be to use an anaconda environment for gromacs purposes, so that gromacs will be isolated from linux system if something goes wrong.
What if the force field is other than CHARMM36?
That you have to work out by trial and look for the documentation of it 👍
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?
Pls check your networkx version. It should be 2.3. Try this...
Use correct python version either python 3.5.2 or 3.7.3
@@pymolbiomolecules my pyhton version is 3.10... How can i install the 3.5.3 version? thank you
Why did you change 167 to 1?
Because as it is the first residue in this file. So as per sequential order we should give 1 👍
Which numpy version is required?
the numpy that comes default in operating system is enough. But networkx version2.3 is must sir
I have a problem: cannot import name 'gcd' from 'fractions' (/usr/lib/python3.10/fractions.py). Thanks
may be due to networkx or python3 error so try using correct versions of both
did you solve your issue ?
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, 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?
yes that may be due to networkx or python3 error. So try using python 3.8 and networkx 2.3 👍
@@pymolbiomolecules i am having the same problem .Did you solve your issue ?
i am having the same problem .Did you solve your issue ?
@@tanverhasan7059 Same, working with python3.8 and networkx 2.3 and still having the issue.
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?
you have defaulty python 3.10. When you install networkx==2.3 it will install to python 3.10. But in this tutorial, it is shows for python 2.7.
Try to use Python 3.x and networkx 2.3 it will solve your issue
I'm using Python3.10 and networkx 2.3, still have same problem. Please help.
@@pymolbiomolecules