VMD-L Mailing List

From: Dong Luo (us917_at_yahoo.com)
Date: Wed Dec 21 2011 - 11:13:26 CST

I use such a script recently and attached here.

Assuming you already loaded the simulation trajectory into VMD, after source this tcl file in the tk console, type
contactFreq "selection for protein" "selection for ligand"
to get the residue based contact frequency output to the tk window. Here assume contact is defined as < 4 angstrom distance. Check script for other options.

Dong

________________________________
 From: flavio seixas <oivalf_nix_at_yahoo.com>
To: VMD List <vmd-l_at_ks.uiuc.edu>
Sent: Tuesday, December 20, 2011 9:10 AM
Subject: vmd-l: Protein-ligand contact
 
Hello,
I ran a molecular dynamic simulation of a protein-ligand system.
Now, I want to know which residues of the protein had a higher frequency of contact with the ligand along the simulation.
Is there any script for this kind of analysis?
I appreciate any help.

Regards,

Flavio