That is not correct if you intend to look at protein:lipid interactions, unless you have a new trajectory created with MERGE COOR RECENTER. Regardless of whether the analysis is geometric or energetic, if you move the system to center the protein, if it was protruding from the unit cell, there will be many missing lipids UNLESS you do an image update to repack the lipids. How do you intend to recenter w/o the crystal information?
Also, COOR HBOND is only image aware if if you've set up images.
