Dear Pymol users!


I want to examine protein-ligand interactions observed in the md trajectory using Pymol.

For such task I have 100 snapshots of the protein-ligand complex which I've loaded into the pymol. Now I want to extract from all snapshots 100 ligands as the separate 100 objects and save it in the mol2. Actually I can do such task in the simplest way extracting all ligands in one object but I need as a result 100 mol2 files. Could someone show me example of some script which could do such tasks?

Also I'll be very thankful if someone can provide me with some tool which can be used for investigation of the ligand dynamics along MD trajectory ( in particular I want to visualize all binding poses and define all polar contacts along trajectory). For such task I've being used pymol as well as pose view loading snapshots to that programs but that way is not appropriate for analyzing of the ensembles of the binding poses obtained from md run.


Thanks for help,


James