Comments (3)
Hello all
I faced the same problem
[05:39:16] Explicit valence for atom # 1 O, 3, is greater than permitted
ArgumentError Traceback (most recent call last)
in <cell line: 122>()
187 out.close()
188 hmol = Chem.MolFromMolFile('temp.mol', removeHs=False)
--> 189 charge_mol = Chem.rdPartialCharges.ComputeGasteigerCharges(hmol)
190 charge = Chem.GetFormalCharge(hmol)
191 print("Charge = " + str(charge))
ArgumentError: Python argument types in
rdkit.Chem.rdPartialCharges.ComputeGasteigerCharges(NoneType)
did not match C++ signature:
ComputeGasteigerCharges(RDKit::ROMol mol, int nIter=12, bool throwOnParamFailure=False)
from making-it-rain.
Hi All,
Sorry for the delay.
You have issues on your ligand PDB file, RDkit library is not able to read and compute the charges of your molecule. Can you please double-check your input file?
Thank you.
from making-it-rain.
Hi,
Sorry for the delay. The previous code was not able to compute the charges correctly. Now, I've changed the notebook, and you can assign the charge of your molecule.
Please let me know if it's working fine.
Thank you.
Best,
Pablo
from making-it-rain.
Related Issues (20)
- Having Issues with the AlphaFold2+MD notebook about "no module named colabfold" HOT 1
- Error in Protein_ligand.ipynb antechamber commands HOT 3
- Hydrogen added to ligand against intent?
- Ligand parameterization panda code error HOT 2
- Protein_ligand.ipynb PDBFixer problem HOT 2
- Hi, Pablo sir kindly help me with running metalloproteins - ligand complex. I don't find a way to run them. Please suggest me what should i do now?
- Continuing trajectory analysis from previous MD simulation HOT 1
- Protein+Membranes.ipynb | Parameters to generate the topology HOT 1
- Martini+cg2all.ipynb | Parameters to generate the Martini topology HOT 1
- can't install dependencies
- RMSD
- Simulating a metallo-protein Apo form
- PDB database structure containing small molecules with certain pattern not working in protein_ligand notebook
- Protein_ligand.ipynb
- Issues regarding scripts to run MD Simulation HOT 2
- Hbond and SASA
- checkpoint frequency is "savcrd_freq" ? HOT 1
- Glycam.ipynb Error generating Amber Topology HOT 1
- Can't run protein-nanoparticle simulation. HOT 1
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from making-it-rain.