Hello,
When I ran LigandFit (with "energy minimisation of ligand in protein" option checked)from a SD file containing several ligands (built and minimized before docking), I obtained strange pose results such as aromatic cycles that are not in a plane (e.g. with tyrosine)or completely distorted (with a naphtalene group).

However, when such compounds are docked separetely (not collected in a SD file), these problems are not encountered.

What could cause such problems ?
Thanks.