Using AFLP
The usage of AFLP is the same as the usage of AdaptiveFlow in general, which is described here.
All specific options/features which one can activate/configure in AFLP are described in the control file tools/templates/all.ctrl, where the values for all of them can be specified. These options/features include:
Neutralization
Desalting
Tautomerization
Protonation
3D Conformer Generation
Target Format Generation
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