Navigation: Home > How to generate a molecule file? Welcome to DDI-CPI!

How to prepare a molecule file?

1. Let's take "Abacavir" as an example. First search "Abacavir" in PubChem Compound. Select the right molecule and find "Isomeric SMILES" of this molecule (if not exist, use "Canonical SMILES").

2. You can now directly submit this SMILES code to our server.

[Optional] If you want to use Corina to generate its 3D structure, copy the SMILES into Corina and submit to achieve the 3D structure of the molecule.

Download the molecule as PDB file and submit it to our server.

3. [Optional] If you want to prepare a mol2 file, add charges of your molecule using Vega ZZ.

Since the generated molecule contains hydrogens, we only need to add charges: Left toolbar -> Charges Potential (recommended Force field: "CHARMM", Charges: "Gasteiger") -> Hit "Fix";

Save as: Abacavir.mol2. You can submit mol2 files to our server as well. Please note you only need to submit one format (SMILES/PDB/MOL2) for each molecule file. This is just a demo and you don't have to go through all the steps.