ATB - Automated Topology Builder and Repository

The ATB automates the generation of classical molecular force field parameters for user-submitted compounds. For a list of frequently asked questions, see the FAQ.

Using the ATB

• Overview of the ATB
• Registering for an ATB Account
  • Password
• Searching for Molecules
  • Structure Search
    • Match Found
    • No Match Found
  • Database Search
  • Comparing Molecules
• Submitting New Molecules
  • Submission Process
  • Using JSME and JSmol
  • Using SMILES
• Downloading Outputs
  • Method 1
  • Method 2

About the ATB

• Methodology
• Feature List
• References

OFraMP

• About OFraMP
• Importing a Molecule into OFraMP
• Shell size
• Selecting Fragments
• Missing Charges
• Manually changing the charge of an atom
• Saving Your Progress
• Sending Charges to the ATB
• Downloading Coordinate and Topology files

The Containerized ATB

• Using the ATB as a Container
• Installation Prerequisites
• Installing Docker
• Installing and Starting the ATB
• Installing GAMESS
• Initializing the ATB Database
• Adding New Users
• Committing Changes to a Container
• Updating the ATB