Re: [PyMOL] Visualization of the protein-ligand interactions

[Thomas E. <te...@gm...>]

> 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?
>
>
Save all ligands in a multi-mol mol2 file and then split if with fconv -s.

http://pc1664.pharmazie.uni-marburg.de/download/fconv



> 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.
>
>
I usually monitor H-bonds with g_hbond from GROMACS Tools and Salt-Bridges
with the respective VMD plugin. Then I make a table with frequences of each
polar interaction, pick up a frame that contains as many important
interactions as possible, load it in PyMOL and draw dotted lines between
the interacting atoms.

PS: I didn't know about PoseView plugin, it seems to be a very useful
addition to PyMOL :)

Thomas

-- 

======================================================================

Thomas Evangelidis

PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE

email: te...@ph...

          te...@gm...


website: https://sites.google.com/site/thomasevangelidishomepage/