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
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