Transmembrane

Step 1: Platform Manipulations

Model Generation

Model Simulation and Analysis

Step 2: Choose the Type of Lipids (! Please enter the lipid counts)

Note: Please find your lipids according the name rule in the lipid database (http://formulationmm.computpharm.org/database/lipid_database_for_transmembrane)

Selected Lipids

No Lipids selected

{{ polymer.displayName }} Count:

Available Lipids ({{ availablePolymers[selectedPolymerType].displayName }})

Available Lipids (No Selection)

Step 3: Drug Input

SMILES:

PDB files:

Electrical Charge:

Note: Please add hydrogen atoms and define the charge for your molecule before submission!

Step 4: Model Conditions

Box Size Z (nm):

Note:You should hold the distance of Z aixes long enough if you will run umbrella sampling (more than two times of your pull disantance). If pull distance is 8 nm, length of Z axies should be over 16 nm.

Distance (nm):

Note: Here you can define the distance between drug and membrane. 0 nm indicate the drug in the center of membrane.

Temperature (K):

Note: Model generation will complete in 1-2 minutes.
Model simulation will complete more than half an hour (based on the system size)

MUST READ before process:
You always need to run several turns model generation to obain an ideal model. So don not run model simulation and analysis until you obtain an ideal model. Welcome to contact us (um.formulationmm@gmail.com) if you have any questions.