Forcefield for simulating peptide with heparin!!!!

From: Aditya Ranganathan (aditya.sia_at_gmail.com)
Date: Mon May 02 2011 - 07:24:56 CDT

Hello,

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 ?

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

Regards,

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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