Hello, I am an academic student using DS 2.1.  I am trying to use interaction filters (along with LigandFit) to basically save only poses with selected interactions between the ligand and the protein receptor.  The ligand contains an amidine group which has two hydrogen bond donors that interact with a carboxylate group of the receptor.  The problem is that the conformations that I'm getting with the use of interaction filters are not the ones I am looking for.  The amidino group is positioned orthogonally (undesired) instead of linearly (desired).  Attached is a snapshot of the work station that I use.  It displays the ligand (highlighted in yellow) and the carboxylate group of the protein (also in yellow) and you can see the pose that I want to keep.  The reason is that I am working with another protease that has similar homology and using an analogous inhibitor.  But I want DS to save a pose that is similar to trypsin & its inhibitor (the file is 1MAY in the protein data bank).  Any help would be appreciated.

-AK