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

[James S. <jms...@gm...>]

Thomas, thanks for help!


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 ?

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) ?

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).


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/
>
>
>
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