Fields are a feature of the XED/COSMIC software. They are uniquely constructed via the use of XEDs (eXtended Electron Distributions) which were specially developed for Field generation. More discussion on Fields and XEDs will be found in Section 2.
It is recommended that ion-pairs are created where you expect the molecule to be charged (as an anion or cation)
You can generate a field on a molecule with ACCs (atom centred charges) or XEDs. The former are not very instructive and are often misleading.
This routine creates a field on the currently displayed molecule. The procedure is relatively fast and is therefore allowed to proceed on-line.
Click the button and answer the questions.
The log output is not usually necessary.
You can calculate any one of the 3 probes individually. It is usual to calculate all three.
You can probe the surface with all sorts of neutral groups. For drug design, the default for a peptide/protein environment seems sensible.
With two fields on screen (see Book 7 for reading more than 1 file) , this button attempts to overlay one field on another. This is a 'one-shot' procedure and does not always give the best results. More elaborate overlay techniques are being investigated for this function.
The returned overlay 'energy' is a measure of the goodness of fit. It is not really an energy. The overlay techniques use a coulombic-type potential to maximise overlay of field points. The field points themselves are extrema (maxima and minima) of energy wells and are therefore true energy values. The unit of overlaying of two such wells is thus energy2/distance.
