Editing ChargeCalculator:Job submission (section)

==Pick EEM parameters==

The Electronegativity Equalization Method (EEM) is the procedure by which atomic charges are calculated. EEM employs special parameters for each type of atom. An [[ChargeCalculator:Terminology | ''EEM parameter set'']], or simply ''set'', was developed for a certain charge definition, and contains parameters for certain atom types (H,C,N,O, halogens, metals, etc, depending on the target molecules). 

Many EEM parameter sets have been published in literature, and are available here as ''built-in sets''. '''ACC''' tries to recommend an EEM parameter set suitable for the molecules you uploaded. It may be that the default '''ACC''' selection is not optimal for you, or you wish to try several EEM parameter sets. Click ''more'' or ''Show sets'' for a table with the full list of sets available in '''ACC'''.

The applicability domain of a given EEM parameter set is generally limited to the target molecules, and closely related to the applicability domain of that particular approach. This is why the table with EEM sets is organized according to the class of ''target molecules'' (organic molecules, biomolecules), and the charge definition, or ''approach'' used during the development of the parameters (population analysis, QM theory level). Click on the name of any set to get more info (citation, target molecules, approach) in the panel on the right side of the table. In order to view the parameters themselves, click ''View XML''.

In the table with EEM sets, check the column ''Atoms'' to see which atom types are covered by each set. '''ACC''' will let you know if a given set does not contain parameters for some atom types present in the molecule(s) you uploaded. Look for the orange highlight which marks <span style="color:#DAA520">missing parameters</span> in the column ''Missing atoms''. If parameters are not available for a certain ''atom type'', these atoms will be skipped during the EEM calculation. Note that if built-in EEM sets with all necessary parameters are available, the rest of the sets are hidden by default. To reveal them, untick the option ''Show only sets with all required parameters'' at the top of the table with sets.

Select one or more EEM parameter sets for your computation. Pick sets which contain EEM parameters for all or most atoms in your input molecule(s), and which have lower values of the ''priority'' descriptor. Each EEM parameter set will be associated with a different '''ACC''' job or set of jobs.

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 |<!--Col1-->EEM employs special parameters for each ''atom type''. '''ACC''' tries to recommend an EEM parameter set suitable for the molecules you uploaded.
 |<!--Col2-->You may pick one or more EEM parameter sets for your calculation.
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You may also ''add'' your own set of EEM parameters if you are unhappy with the built-in sets available. Click the ''Add'' button at the top of the ''EEM Parameters'' section to open a separate window where you can fill in the values of the parameters into a predefined XML template suitable for '''ACC'''. Make sure to keep the established XML syntax and give your set a unique name, then click the ''Add'' button. '''ACC''' will verify the syntax and let you know if you need to change anything. Your new set will be available in the table, along with the built-in sets.

You can use the ''add'' function in order to generate modified versions of built-in sets. Click on the built-in set of interest, then ''View XML'' on the panel to the right. Copy/paste the content into the ''Add'' window and make your modifications. For example, if you copy the parameters for H into the same set, and modify the ''Element name'' tag to say P, you have added EEM parameters for phosphorus which are identical to the EEM parameters used for hydrogen. Save this EEM parameter set under a unique name, and it will be available in the table. 

This strategy is very useful if the EEM parameter set you wish to use does not contain parameters for certain atom types present in your molecule(s), or if '''ACC''' could not read chemical elements from the atom type information in the input file, and reported an <span style="color:#DAA520">''unknown chemical elements'' warning</span>. You must always check the ''Message'' column in the table with molecules, to ensure that all relevant atoms are included appropriately in the calculation.

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