I am using LigPrep to prepare 3D ligands for modeling. How do I generate only a single output structure per input structure?

Due to the expansion stages, LigPrep does not have a dedicated mechanism to ensure that there is only a single output structure per input structure. Below are two ways to run LigPrep that should almost always result in one output structure per input structure. The stereochemistry feature "-ns" can be used instead of "-s 1". The former does not place constraints due to stereocenters. The latter produces an isomer that best matches natural product chemistry.
With Ionizer:

$SCHRODINGER/ligprep -i 2 -W i,-ph,7.4,-pht,2.0,-mo,1 -s 1 -r 1 -nt -bff 14 -isd input.sdf -omae test-out.maegz

With Epik:

$SCHRODINGER/ligprep -i 2 -epik -We,-ph,7.4,-pht,2.0,-ms,1 -s 1 -r 1 -nt -bff 14 -isd input.sdf -omae test-out.maegz

Keywords: LigPrep

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