(no subject)

From: Nicolas Sapay (nicolas.sapay_at_cermav.cnrs.fr)
Date: Tue May 03 2011 - 11:51:42 CDT


Le 02/05/2011 14:24, Aditya Ranganathan a écrit :


I had tried to simulate a system of peptides and its interaction with
glycosaminoglycan molecules like heparin. I came across an interesting
publication where a group has used MD simulation to study heparin
interaction with Abeta42 peptide (
http://www.fasebj.org/content/24/11/4250.abstract). However, they have used
AMBER forcefield for the same.

I would like to know how I would approach my problem if I were to do this
using CHARMM forcefield. Is it possible to generate a psf file of a system
containing peptides and heparin. Which topology and parameter files should I
use to achieve the same. Please suggest a protocol to go about this and
please share any available forcefields for heparin/glycosaminoglycans. Does
a topology/parameter file for the same exist ?

Glycosaminoglycans are highly difficult to parameterized, particularly
heparin/heparan sulfate, and there is no standard protocol to do that. If
you wish to quickly obtain parameters for heparin, you should directly
contact the authors of the publication. You can use AMBER topologies with
NAMD, there is a paragraph about that in the manual.


Any sample .pgn file for the same would be of great help.


Srivastav Ranganathan
M.Tech Student (Environmental Science and Engineering) and Research
Assistant (Biosciences and Bioengineering)
Indian Institute of Technology Bombay (IIT Bombay)
Mumbai, India

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