> Chimera's Viewdock can input a mol2 file containing many ligands, and
> determine minimum binding energy for a specific receptor's pocket for each
> ligand. Can OB perform energy minimization of ligands in batch mode (loop)
> and then export all ligands to a single mol2 file?
Sure.
% cat >ligands.smi
CCC
COC
CO
CCCS
% obabel ligands.smi -O ligands.mol2 --gen3d --minimize
4 molecules converted
Hope that helps,
-Geoff
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