ACC: First Time Guide

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.

Calculate atomic charges in 3 easy steps

Help...

Help...

2

Upload your protonated molecule in a supported format: pdb, pqr, mol2, mol... Upload multiple molecules as .zip

Help...

Help...

Help...

Step 1 – Upload molecule(s)

3

Once you chose the input file with molecule(s), click Upload.

Step 1 – Upload molecule(s)

4

Help...

Help...

Help...

Help...

Once you upload your molecule(s), ACC tries to prepare a default setup, so you can start your calculation immediately...

Step 2 – Setup

5

Start calculation

using default setup

… or check and adjust

the setup

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 – Setup

6

Check and adjust the

setup

Help...

Check the total molecular charge (default=0)Check the messages (missing H, suboptimal formatting...)

Total molecular

charge

Step 2 – Setup

7

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 – Setup

8

Help...Step 2 – Setup

For biomacromolecules, ACC provides time and memory efficient implementations of EEM. Click Add to pick a suitable method.

Efficiency

9

Help...Step 3 – Start

Keep the default settings or make your adjustments, then start the calculation 10

… try any of the multiple

interactive guides

... check the tool tips

… consult the Wiki manual

Got lost during setup?

11

Download structure files with charges (mol2, pqr...), statistics.Unique URL available for later access

Retrieve results

12

URL

Help...

Alternatively, for each molecule you can examine the results directly in your browser...

Help...

URL

Retrieve results

13

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

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 – Raw Data

Molecule

Unique set of charges, resulted from a job or read in from the input file

15

Interesting statistics available for atomic and residue charges

Help...

Examine results for each molecule – Analyze

Molecule

The charge on the Mg ions does

not vary much

16

Help...

Examine results for each molecule – Compare

Molecule

Comparison between sets of charges resulted from different jobs, or read from the input file 17

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 – 3D Model

Molecule

Several visualization options to help interpret the results

18

… try any of the multiple interactive guides

... check the tool tips

… consult the Wiki manual

Need help with interpreting the results?

19

Help...

Help...

Try the setup examples, with detailed explanations...

Don't know where to start?

20

… or view the setup and results for a few interesting computations...

Help...

Don't know where to start?

21

Help...

Help...