Editing ChargeCalculator:Job submission (section)

=Setup computation=

Once you have uploaded your molecule(s), ACC parses the molecular structure and redirects you to the '''ACC Setup page'''. Note that at this point a ''unique URL'' has been generated on the ACC server, and assigned to your computation. You may use this URL during calculation setup, execution or completion to access all the data associated with your '''ACC''' computation.

{| class="wikitable" border="1" style="margin: 1em auto 1em auto;" width="650px"
 |-
 |<!--Col1-->[[File:ACC FirstTimeUserGuide 05.jpg| 650px]]
 |<!--Col2-->[[File:ACC FirstTimeUserGuide 06.jpg| 650px]]
 |-
 |<!--Col1-->Upon uploading the molecule(s), ACC parses the molecular structure and tries to prefill the submission form with suitable default settings.
 |<!--Col2-->Check and adjust whatever default settings you find unsuitable.
 |}

ACC generally tries to prefill the setup form with suitable options based on the molecule(s) you uploaded. It commonly happens that you can start the calculation immediately after loading the molecule. Nonetheless, the setup has a few critical sections you should check and maybe adjust before proceeding.

==Set total charge==

[[File:ACC FirstTimeUserGuide 07.jpg|thumb|right|650px|The total molecular charge correlates with the number of unsatisfied valences in the molecule. Make sure to assign the appropriate total charge for all non-neutral molecules you uploaded.]]

The total molecular charge quantifies the amount of electron density that will be distributed across the molecule during the EEM calculation. The total molecular charge plays an important role in the quality of the '''ACC''' results. By default, '''ACC''' assumes that all molecules are neutral. If this is not the case for your molecule(s), you must indicate so in the appropriate field. For each non-neutral molecule you uploaded, write the appropriate total charge value in the ''Total charge'' column. If all molecules you uploaded have the same charge, use the ''Total Charge for All Molecules'' field, and click ''Apply''.

The total molecular charge must be in tune with the structure of the molecule. Specifically, it correlates with the number of unsatisfied valences in the molecule. For this reason, '''ACC''' checks valences, and produces a <span style="color:#DAA520">''missing H'' warning</span> if they are not satisfied, suggesting the molecule may not be neutral. You should always check the ''Message'' column.
<br style="clear:both" />

==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.

{| class="wikitable" border="1" style="margin: 1em auto 1em auto;" width="650px"
 |-
 |<!--Col1-->[[File:ACC FirstTimeUserGuide 08.jpg| 650px]]
 |<!--Col2-->[[File:ACC EEM sets.png| 650px]]
 |-
 |<!--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.
 |}

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.

<br style="clear:both" />

==Pick computation method==
[[File:ACC FirstTimeUserGuide 09.jpg|thumb|right|650px| In addition to classical EEM, '''ACC''' offers two time and memory efficient EEM implementations. Please use ''EEM Cutoff'' for systems with tens of thousands of atoms, and ''EEM Cutoff Cover'' for larger systems, in both cases with a ''Cutoff Radius'' parameter of at least 8.]]

The default computation includes all atoms in the system and solves the entire EEM matrix in double precision. For very large systems you may need to resort to one of the time and memory efficient EEM implementations specifically tailored for such systems (check the [[ChargeCalculator:Theoretical_background | Theoretical background ]] for more details). By default, '''ACC''' tries to suggest a computation method suitable for the molecule(s) you uploaded.

You may change the method chosen by default, and ''add'' one or more methods of your choice using the ''Add'' button at the top of the ''Computation Methods'' section. Note that each unique method configuration added to the list will result in an additional '''ACC''' job, or set of jobs.

Even for molecules containing several thousands of atoms, our implementation of EEM is very time efficient, and you may use the method labeled as ''Full EEM''. For systems with tens of thousands of atoms, you will probably need to pick ''EEM Cutoff'', and a reasonable value for the ''Cutoff Radius'' parameter (we recommend a minimum of 10). A biomolecular complex with hundreds of thousands of atoms makes good use of the method ''EEM Cutoff Cover'' with a ''Cutoff Radius'' of 8 and ''single Precision''.

If your system is solvated or includes a few key water molecules, you may want to run parallel calculations with and without the water molecules (tick the ''Ignore Waters'' option), to see how water can affect the charge distribution in the biomolecule.  Note that '''ACC''' identifies water atoms if they are annotated by a residue name typically associated with water (HOH, WAT, H2O). Other residue names sometimes associated with water, such as SOL and TIP, are not considered here because the Protein Data Bank contains instances of such residues which are chemical components different from water. Thus, if you wish to ignore water which is annotated in your file as SOL or TIPx, you will need to remove these records before submitting to '''ACC'''.

<br style="clear:both" />