Cyclodextrin

Step 1 · Select Platform Manipulations

Model Generation is required before downstream steps

Model Generation

Model Simulation and Analysis

Step 2 · Define Cyclodextrin Host

Use a predefined entry from our database or upload a custom host for GAFF2 parameterization

Click a chip to preview its structure

Cyclodextrin Host SMILES

The host will be built and parameterized with GAFF2

Upload one structure file with extension .pdb .mol2 .sdf .gro

Host Net Charge

Host Charge Model

Outputs will be standardized as cyc.pdb cyc.itp cyc.gro

Step 3 · Define Model Conditions

Temperature (K)

Used in topology generation and default mdp templates

Step 4 · Define Drug Molecule

Provide the ligand and select a charge model for GAFF2 parameterization

SMILES

Choose Structure File

Net Charge

Charge Model

RESP provides higher accuracy; AM1-BCC is faster and stable

Model generation takes ~1–2 minutes; simulation ~5–8 minutes

Perform multiple rounds of Model Generation to obtain a stable host–drug complex before running Simulation and Analysis. For support contact um.formulationmm@gmail.com.