ACC: First Time Guide
- 1. AtomicChargeCalculator - ACC First Time User Guide DO: calculate, visualize and analyze WHAT: atomic charges which respond to changes in molecular conformation and chemical environment WHERE: biomacromolecules and drug-like molecules.
- 2. Calculate atomic charges in 3 easy steps Help... Help... 2
- 3. Upload your protonated molecule in a supported format: pdb, pqr, mol2, mol... Upload multiple molecules as .zip Help... Help... Help... Step 1 C Upload molecule(s) 3
- 4. Once you chose the input file with molecule(s), click Upload. Step 1 C Upload molecule(s) 4 Help... Help... Help...
- 5. Help... Once you upload your molecule(s), ACC tries to prepare a default setup, so you can start your calculation immediately... Step 2 C Setup 5 Start calculation using default setup or check and adjust the setup
- 6. Help... A default setup may not be available, or may not be optimal for your calculation. Check and adjust each section of the setup... Step 2 C Setup 6 Check and adjust the setup
- 7. Help... Check the total molecular charge (default=0) Check the messages (missing H, suboptimal formatting...) Total molecular charge Step 2 C Setup 7
- 8. Help... EEM is an empirical approach used to calculate atomic charges. Click Show sets to list all EEM parameter sets available in ACC. EEM parameters Step 2 C Setup 8
- 9. Help...Step 2 C Setup For biomacromolecules, ACC provides time and memory efficient implementations of EEM. Click Add to pick a suitable method. Efficiency 9
- 10. Help...Step 3 C Start Keep the default settings or make your adjustments, then start the calculation 10
- 11. try any of the multiple interactive guides ... check the tool tips consult the Wiki manual Got lost during setup? 11
- 12. Download structure files with charges (mol2, pqr...), statistics. Unique URL available for later access Retrieve results 12 URL Help...
- 13. Alternatively, for each molecule you can examine the results directly in your browser... Help... URL Retrieve results 13
- 14. A job is defined by its unique setup (total molecular charge, set of EEM parameters, computation method), and produces a unique set of charges. Help... Examine results for each molecule - Summary Molecule Input and computation warnings Basic info about the computation 14
- 15. The charges can be inspected at two levels of resolution: - atomic charges - residue charges (sum of atomic charges per residue) Help... Examine results for each molecule C Raw Data Molecule Unique set of charges, resulted from a job or read in from the input file 15
- 16. Interesting statistics available for atomic and residue charges Help... Examine results for each molecule C Analyze Molecule The charge on the Mg ions does not vary much 16
- 17. Help... Examine results for each molecule C Compare Molecule Comparison between sets of charges resulted from different jobs, or read from the input file 17
- 18. 3D model built using: - atomic positions, colored by atomic charges or charge differences - residue positions, colored by residue charges or charge differences Help... Examine results for each molecule C 3D Model Molecule Several visualization options to help interpret the results 18
- 19. try any of the multiple interactive guides ... check the tool tips consult the Wiki manual Need help with interpreting the results? 19
- 20. Help... Help... Try the setup examples, with detailed explanations... Don't know where to start? 20
- 21. or view the setup and results for a few interesting computations... Help... Don't know where to start? 21 Help... Help...