Editing ChargeCalculator:Technical details (section)

==Implementation related==

===Structure===
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'''.

'''ACC''' produces a <span style="color:#DAA520">''missing H'' warning</span> if no protons are detected in the input file. Despite the warning though, '''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.).

===Total charge===
The total molecular charge plays an important role in the quality of the '''ACC''' results, as it quantifies the amount of electron density that will be distributed across the molecule during the EEM calculation. The total molecular charge must be in tune with the protonation states. '''ACC''' assumes by default that all molecules are neutral, and it is the user's responsibility to mark the charged molecules with their correct total charge.

===Parsing===
'''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. 

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 <span style="color:#DAA520">''unknown chemical elements''</span>, 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.

'''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'''.


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