VMD-L Mailing List

From: flavio seixas (oivalf_nix_at_yahoo.com)
Date: Mon Apr 30 2012 - 18:29:17 CDT

Hi Dong,

Many thanks for your help.
Your script works very fine.

Regards,

Flavio

--- On Wed, 12/21/11, Dong Luo <us917_at_yahoo.com> wrote:

From: Dong Luo <us917_at_yahoo.com>
Subject: Re: vmd-l: Protein-ligand contact
To: "flavio seixas" <oivalf_nix_at_yahoo.com>
Cc: "VMD List" <vmd-l_at_ks.uiuc.edu>
Date: Wednesday, December 21, 2011, 5:13 PM

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, typecontactFreq "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