Re: aromatic-aromatic interaction

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Fri May 30 2008 - 06:57:51 CDT

Hi Ramya,

Please check out the following reference:

Gervasio FL, Chelli R, Procacci P, Schettino V. Proteins. 2002, 48, 117-125.

There are some good geometric definitions for aromatic-aromatic
interactions between different aminoacid pairs.

Based on my own experience, you should take into consideration not
only centroid-centroid distances, but also interplanar angles to
correctly identify aromatic-aromatic interactions.

Cheers,
Michel

On Thu, May 29, 2008 at 7:20 AM, ramya narasimhan <ramya_jln_at_yahoo.co.in> wrote:
> Hi all,
> Is it possible to find aromatic - aromatic interaction (taking
> centroids) for each structure in a trajectory using NAMD? If possible,
> please suggest me.
>
> Thanks in advance.
> Ramya.L.
>
> ________________________________
> Chocoholics' paradise! Enter here.

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:49:30 CST