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

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

> As I understood fconv can be used for the split several mol2 (or pdb)
> files which was placed in 1 model to the several pdb files, doesnt it ?
>
> fconv can do miracles :) check it out !

fconv -h



> In past I forced with some problems with  g_hbond. Is there any other way
> to monitor h bonds along the trajectory (e.g in vmd) ?
>
>
In contrast, I encountered problems with the H-bonds VMD plugin, that's why
I resorted to g_hbond. Beware that g_hbonds will count the frequencies of
salt-bridges too.


> PoseView is used as the separate software or web server
> http://poseview.zbh.uni-hamburg.de/poseview ( I mean that I analyze polar
> interactions both in pymol as well as via pose view).
>
>
If you find a way to draw the most important protein-ligand interactions
throughout the trajectory with PoseView, then I would be very interested to
know how.


>
> James
>
> 2013/4/24 Thomas Evangelidis <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/