VMD-L Mailing List

From: syma (syma.khalid_at_bioch.ox.ac.uk)
Date: Wed Nov 16 2005 - 02:28:14 CST

Hi Kara,

I guess my reply is not really a vmd one- but you can use 3DNA
(http://rutchem.rutgers.edu/~xiangjun/3DNA/) and
CURVES(http://www.ibpc.fr/UPR9080/Curindex.html) (as well as others) to
characterise DNA structure. Both of these will give you parameters to
measure deviations in the DNA backbone and also the base pairs. I have used
both and they are very straightforward to use.

3DNA lets you monitor parameters over the course of a simulation, CURVES
allows analysis of only one structure at a time so one must calculate
average structures to analyse.

Hope this helps.

-----Original Message-----
From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of
Kara Di Giorgio
Sent: 16 November 2005 01:44
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: Method to measure DNA perterbation

I know this is not exactly a VMD question, but I though the community
may have run across this question before.

Does anyone know of a method to quantify how much DNA has been
perterbed during a MD run? I have done MD simulations of DNA with a
cross-linker of various lengths in it. I need to compare how much each
linker perterbed the DNA. Does anyone have any ideas?

Thank you,

Kara Di Giorgio