Editing ChargeCalculator:Job submission (section)

=Upload molecules=
'''ACC''' is able to read the molecular structure and charge information from the most common file formats. Nonetheless, because it was designed to handle molecules of all kinds and size, '''ACC''' generally requires that the input files follow the formal guidelines established for each format.

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 |'''Checklist for uploading molecules'''
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*File format: PDB, PDBx/mmCIF, PQR, MOL, MOL2, SDF, or .zip with multiple files of a suitable format; 50MB limit for each upload
*All H should be present, according to the appropriate protonation states. The computation can run even when H are missing, but the absolute values of the atomic charges will not be chemically relevant.
*No limitation regarding the size, number or nature of the chemical entities in each file: proteins, nucleic acids, ligands, water... - everything will be loaded and identified as a single ''molecule''
*If a file contains multiple molecules annotated as such (typically NMR models), only the first one will be loaded. If you want to load more NMR models (e.g., to later compare the results), you need to upload them in separate files.
*If a molecule contains more ''chains'', the chain IDs should be present at their appropriate location.
 |}

{| class="wikitable" border="1" style="margin: 1em auto 1em auto;" width="650px"
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 |<!--Col1-->[[File:ACC FirstTimeUserGuide 03.jpg| 650px]]
 |<!--Col2-->[[File:ACC FirstTimeUserGuide 04.jpg| 650px]]
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 |<!--Col1-->ACC supports all popular molecular structure formats (PDB, PDBx/mmCIF, PQR, MOL, MOL2, SDF). For multiple molecules, upload a .zip archive. All structural elements in one file are assigned to one molecule (protein, ligands, water, etc.).
 |<!--Col2-->Make sure the input molecules are complete. If necessary, use an external program to add H before uploading the molecule(s).
 |}

All the chemical entities in each file (proteins, nucleic acids, ligands, water...) will be loaded and identified as a single ''molecule''. If you do not wish to include part of the system in your calculation, you must remove it from the input file. Once you have uploaded the file, you may choose to include/ignore water, but all other chemical entities will be present.

By default, only the first NMR model is loaded from files with multiple models annotated as such. If you wish to load all NMR models, you must produce a single input file per model. The same holds true for multiple molecules in sdf format - only the first molecule will be loaded.

In order to produce chemically relevant atomic charges using EEM, it is necessary that the structure of the molecule be complete. No crucial parts should be missing. If parts of the structure are missing, appropriate cappings should be included. All protons should be present according to the relevant protonation state. Since '''ACC''' does not currently include functionality for editing the molecular structure, you must address these issues prior to uploading the molecule into '''ACC'''. For example, you may use a server like [http://nbcr-222.ucsd.edu/pdb2pqr_1.8/ pdb2pqr] to assign protonation states, add protons and subsequently estimate the total molecular charge.

'''ACC''' produces a <span style="color:#DAA520">''missing H'' warning</span> if no H are found in the input file. Despite the <span style="color:#DAA520">''missing H'' warning</span>, '''ACC''' allows to proceed with the charge calculation step, as it might not always be possible to obtain a perfect structure (e.g., when working with low resolution structures of extremely large complexes). The results from such calculations may not have chemical meaning in their absolute values, but they can be very useful when comparing sets of charges (open vs closed conformation, free vs bound state, etc.).

Input files generally contain ''atom type'' information. Many different atom type schemes are used in different modeling projects. Moreover, many times the output is not even standardized between different applications implementing the same atom type scheme. '''ACC''' attempts to be a general utility, and currently implements only the detection of chemical elements. If the atom types in the input file differ from chemical elements, '''ACC''' will report them as ''unknown chemical elements'', and these atoms will be skipped during the EEM calculation (they will not contribute to the [[ChargeCalculator:Theoretical_background | EEM matrix ]]). A similar problem will arise if the atom type information is not found at the expected place in the file. In the future, a more complex parsing algorithm may be implemented in '''ACC''' in order to cover the most common atom type schemes (e.g., AMBER, OPLS, etc.). Currently, the atom type parsing problem can be worked around either by uploading input files which adhere to the formal guidelines for their respective formats and contain atom types according to chemical elements, or by creating an EEM parameter set with special parameters for those atom types which '''ACC''' finds problematic.

If the chain ID is not explicitly included in the input file, but the molecule contains multiple chains with overlapping residue serial numbers, the results will not be meaningful for the affected residues, and possibly even in the vicinity of these residues. '''ACC''' provides <span style="color:#DAA520">''check chain ID'' warnings</span> both before and after the computation if this problem is detected, so that the input file can be corrected.

If bond information is not explicitly included in the input file, '''ACC''' will attempt to compute this information based on the molecular structure. This algorithm may assign wrong bond information when interatomic distances vary significantly from the expected norms. This behavior may only affect calculations using EEM parameter sets which distinguish between atom types based on bond information.

For a given molecule, you may wish to visualize and analyze atomic charges which you obtained by other means than '''ACC'''. You can use one of the dedicated molecular structure formats that include atomic charges (mol2, pqr). Alternatively, you can use one or multiple wprop files or .*chrg files to supply '''ACC''' with several sets of precomputed charges for one or more molecules. The format of a .wprop file with atomic charges for a molecule with 7 atoms is:

<pre>
molecule name
name of set of charges
Charges
RealAtomProperties
7
1 -0.303792368142346
2 0.172805849402877
3 0.850934507393088
4 -0.665816273614449
5 0.155665455717068
6 0.0563610400635921
7 0.205393963483477
</pre>

To let '''ACC''' know which .wprop or .*chrg files should be assigned with which molecule, you must name these files as '''MOLECULENAME_ref_UNIQUENAME.wprop''' or '''MOLECULENAME_ref_UNIQUENAME.wprop'''. The first part of the file name, ''MOLECULENAME'', must be the same as the name of the molecular structure file containing the molecule to which the set of charges will be assigned. The designation ''ref'' marks this set of charges as user defined. The last part of the file name, ''UNIQUENAME'' is any group of characters which will allow for a unique identification of this set of charges. Thus, if you are uploading the file 4DRP.pdb and wish to include 3 sets of charges that you previously computed using other means, simply name these files 4DRP_ref_1.wprop, 4DRP_ref_2.wprop and 4DRP_ref_3.wprop.

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