Rendering tool of cube file on jupyter-notebook #psikit #psi4 #memo

Visualize molecular orbital is one of the good way for understating molecular reactivity. Opensource quantum chemistry package ‘Psi4’ can generate cube file for MO rendering and psikit has function for rendering MO with pymol. Here is an example notebook.https://github.com/Mishima-syk/psikit/tree/master/examples/Rendering_Orbital_in_PyMol And recently I found new tool for cube file rendering named fortecubeview package. The license ofContinue reading “Rendering tool of cube file on jupyter-notebook #psikit #psi4 #memo”

Advertisement

Molecular fragmentation tool for quantum chemical torsion scan #open_force_field #RDKit

As many reader knows that quantum chemical(QC) calculations are useful and important to determine conformational distributions of small molecules. Because chemists design molecule with not only 2D information but also 3D information. However, computational cost of QC calculation is higher than molecular mechanics(MM) calculations. Last year, Prof. John D Chodera’s group published useful approach forContinue reading “Molecular fragmentation tool for quantum chemical torsion scan #open_force_field #RDKit”

Relation ship between dihedral deg and atomic charge #psi4 #RDKit #psikit

Recently psikit repository got PR about RESP charge calculation. Thanks for PR. And I have question about the relation ship between compound conformation and partial charge. Fortunately, psikit already has an example for torsion scan thank @fmkz___ for sharing useful code. The example code is here. Following code is same as example code linked above.Continue reading “Relation ship between dihedral deg and atomic charge #psi4 #RDKit #psikit”

Use ORBKIT for rendering MO #orbkit #rdkit #psikit #quantum_chemistry

As you know, there many packages for quantum chemistry not only commercial software but also free tools. And each soft has own output format. So user need to understand how to use it. But it is very time consuming step I think. ORBIKIT is a modular python toolbox for cross-platform post processing of quantum chemicalContinue reading “Use ORBKIT for rendering MO #orbkit #rdkit #psikit #quantum_chemistry”

Make input file for geomeTRIC #openbabel #psi4 #geomeTRIC

geomeTRIC is code for molecular structures geometry optimization. TRIC means translation-rotation-internal coordinate (TRIC) system. As described in their publication, geomeTRIC can optimize molecular geometry rapidly and few iteration numbers. It seems useful for Quantum Chemistry. And geomeTRIC supports many QC engines Q-Chem, TeraChem, Psi4 andMolpro. I like psi4 so I tried to use geomeTRIC withContinue reading “Make input file for geomeTRIC #openbabel #psi4 #geomeTRIC”

Quantum Chemistry data of drug bank #QCportal #Quantum_Chemistry

I’m still learning QCArchive. I posted qcportal with reaction dataset. And today I tried to retrieve of drug bank from qcportal. QCportal provides not only calculated numeric data but also 3D mol view by using py3Dmol. OK let’s go to code. get_molecule method provides many data from qcportal web server. What kinds of data inContinue reading “Quantum Chemistry data of drug bank #QCportal #Quantum_Chemistry”

Open data source of Quantum chemistry! #qcportal #rdkit #cheminformatics #quantum_chemisry

In RDKit UGM 2019, I had interest about QCArchive. QCArchive is MolSSI quantum chemistry archive. It provides useful data and python packages. By using one package named qcportal, we can access huge data source of quantum chemistry. It is very useful because QC calculation is useful but it requires computational cost. QC data is usefulContinue reading “Open data source of Quantum chemistry! #qcportal #rdkit #cheminformatics #quantum_chemisry”

Call psi4 from web app! #Psi4 #QuantumChemistry

Psi4 is a python package for quantum chemistry. I like it. Native psi4 has some difficulties for preparing input file. So psikit is useful I think. And I think webmo is useful package for calling psi4. I’ve always been interested webmo. So I tried to use it today.Basic function of webmo is provided free licence.Continue reading “Call psi4 from web app! #Psi4 #QuantumChemistry”

Electrostatic Potential Surface(ESP) calculation with GCNN #RDKit #chemoinformatics

ESP is a key feature in Drug Discovery. There are many publications discussing ESP in Drug Design. However getting accurate ESP is time-consuming because it needs high level QM calculations. To reduce the calculation cost of QM, predict quantum nature by using Deep learning is researched. And some days ago, I found interesting article publishedContinue reading “Electrostatic Potential Surface(ESP) calculation with GCNN #RDKit #chemoinformatics”

Calculate solvent effect in Psi4 #psi4 #quantumchemistry

Recently I use not only chemoinformatics tools but also quantum chemistry tool, my favorite is Psi4. Psi4 has many options and plug-ins for quantum calculation. Most setting of calculation is vacuum, but it actually true. So considering the solvent around the molecules is important. Can psi4 perform calculation with solvent effect? Yes! PCMSolver is pluginContinue reading “Calculate solvent effect in Psi4 #psi4 #quantumchemistry”