Editing ChargeCalculator:FAQ (section)

=After uploading my molecule, I got a warning about "missing hydrogen atoms". How will it affect my calculation?=

EEM, the empirical approach used by '''ACC''' to calculate atomic charges, produces atomic charges which respond to changes in conformation and chemical environment. In order to produce chemically relevant atomic charges using EEM, it is necessary that the structure of the molecule be complete. 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 (note that the warning does not appear if at least one H is present 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.).