How can i convert .gjf into smiles format ?

Dear Qurat Ul Ain Khalid,

Hopefully information below will be helpful to you:

Converting a .gjf (Gaussian Input File) into SMILES (Simplified Molecular Input Line Entry System) format involves several steps, as these are two different representations of chemical structures. The .gjf file typically contains information about the 3D coordinates, atom types, and connectivity of a molecular structure, while SMILES is a linear textual representation of a chemical structure. To convert .gjf to SMILES, you would need to perform the following steps:

Generate the 3D Molecular Structure: The .gjf file contains information about the 3D coordinates of atoms in the molecule. You will need software that can interpret .gjf files and generate a 3D molecular structure from it. Gaussian, which generates .gjf files, can also perform this task. You can use Gaussian to optimize the geometry and obtain the 3D structure.

Identify the Molecule: Once you have the 3D structure, identify the molecule you want to convert into SMILES format. This step is crucial because the conversion may yield different SMILES representations for different isomers or conformations of the same molecule.

Use Chemical Informatics Software: To convert the 3D molecular structure into SMILES format, you can use chemical informatics software or libraries. Some popular options include RDKit (open-source) and ChemAxon's JChem. These tools provide functions for generating SMILES from 3D structures.

Convert and Extract SMILES: With the software or library of your choice, load the 3D molecular structure and use its functions to generate the SMILES representation. You may need to extract the specific SMILES string for the molecule you're interested in if there are multiple structures in the input file.

Review and Validate: After obtaining the SMILES representation, review it to ensure it accurately represents the molecule you intended to convert. SMILES notation is a standardized format, so it should be consistent and easily interpretable.

Save the SMILES: Once you are satisfied with the SMILES representation, you can save it as a text file or use it in your chemical informatics or cheminformatics applications.

It's worth noting that SMILES notation is a simplified and linear representation of molecules, and it may not capture all the detailed 3D structural information present in .gjf files. Additionally, the conversion process may not always be straightforward, especially for complex molecules or mixtures. Careful verification of the resulting SMILES representation is essential to ensure accuracy.

Keep in mind that the success of the conversion may depend on the software and libraries you use, as well as the specific content and formatting of the .gjf file.

Tajinder Kumar Saini

Perform Quantum Chemistry Calculation:Use the Gaussian software to perform a quantum chemistry calculation based on the information in the .gjf file. The output of this calculation will include molecular information such as atomic coordinates, bond lengths, and bond angles.

Extract Molecular Information:Extract relevant molecular information from the Gaussian output file (.log or .out). Look for sections that provide atomic coordinates and connectivity information.

Generate 3D Molecular Structure:Use the extracted information to generate a 3D molecular structure. Software tools like Avogadro, PyMOL, or Gaussian itself can be helpful in visualizing and extracting molecular structures.

Obtain SMILES Representation:Use a chemical structure drawing or conversion tool that supports SMILES notation to manually draw or input the 3D molecular structure. Tools like ChemDraw, MarvinSketch, RDKit, or online platforms such as PubChem and ChemSpider allow you to generate SMILES representations.

Generate SMILES:After inputting or drawing the molecular structure, the software tool should provide an option to generate the corresponding SMILES notation. This SMILES string represents the connectivity and arrangement of atoms in the molecule.

Verify SMILES Accuracy:Carefully review and verify the generated SMILES notation to ensure its accuracy and consistency with the original molecular structure.

How can I measure MMP-1 protein activity or protein level from liver tissue?

Binary Logistic Generalized Linear Mixed model in SPSS. Is it doable?

Looking for Materials with high thermal expansion coefficient and high temperature resistance?

Guidelines for survey (question type) analysis?

What are the values needed for gabor filter's parameter for cifar10 data?

Can we block unwanted images during the x-ray prediction?

No title

What techniques can I use to determine the miscibility of polymer blends?

Sample dilution for quantitative analysis using ELISA?

The procedure compute?

Which is suitable for use with Python? MySQL or SQL Server?

Can Virtual Servers (remote dekstop manager) run heavy ANSYS Fluent CFD simulation ?

What is the most suitable server for predicting protein structures in bacteria?

How to resolve Gaussian error termination " Error termination via Lnk1e in F:\G16W\l103.exe" for TS(QST3)?

How to calculate the Atomic Polar Tensor using DFT ?

Access to supercomputer resources in India?

Anyone know how to contact Raymond Streater?

How to obtain Contig sequence from BAM file?

Why we use feature normalization before using the Gaussian kernel in SVM?

Does Gaussian 09W software take too long to give a result if we have a large chemical structure ?