Giter Site home page Giter Site logo

protein_ligand.ipynb about making-it-rain HOT 3 CLOSED

kadhirmn avatar kadhirmn commented on September 22, 2024
protein_ligand.ipynb

from making-it-rain.

Comments (3)

Salahalmulla avatar Salahalmulla commented on September 22, 2024

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.

pablo-arantes avatar pablo-arantes commented on September 22, 2024

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.

pablo-arantes avatar pablo-arantes commented on September 22, 2024

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)

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo 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.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.