lipid bilayer MD simulations

From: Xavier Deupi <>
Date: Wed 7 Mar 2001 06:01:15 -0800

Hi all,

I'm interested in performing MD simulations of membrane proteins in an
explicit water/lipid bilayer environment using AMBER. I guess some of you
are working in this field, so I have some questions for you...

In AMBER distributions and home page, I have only seen mention to lipid
bilayers in one of the examples for roar, where DLPE
(dilauroylphosphatidylethanolamine) is used, with the associated DLP
residue type. However, I haven't found any reference to this residue type
in the parameter files. I guess people also use other models for the lipid
bilayer (DPPC, POPC,...), so my question is obvious... are parameters for
these phospholipids available anywhere?

I have read that united-atom force-fields are quite common for such
simulations. Is this correct? Anybody is using all-atom force-fields? If
so, are parameters available?

Finally, I would like to keep in touch and have some feedback with people
working in this field... you know, it's very hard to learn on your own
(although sometimes it's the best way) :-)

Well, as always, thank you all in advance.


  Xavier Deupi
  Computational Medicine Lab
  Biostatistics Unit. School of Medicine
  Universitat Autonoma de Barcelona. CATALUNYA (Spain)
  Phone : (3493)-581.23.48

From 7 Mar 2001 09:58:54 -0500
Message-id: <>
Date: 7 Mar 2001 09:58:54 -0500
From: Boyd <>
To: AMBER list <>
Subject: Emerging Technologies/COMP 2001
In-Reply-to: <000f01c0a6e3$1dd10b00$>

Dear Colleagues,

The ACS Computers in Chemistry Division (COMP) will hold its
second annual symposium on emerging technologies at the ACS
National Meeting, Chicago, Illinois, USA, August 26-30, 2001.

Abstracts have started arriving for the "Symposium on Emerging
Computational Technologies at the 125th Anniversary of the
American Chemical Society".

A $1000 prize, generously sponsored by Schrodinger, Inc., will
be to be presented for the best talk at the symposium.

You are invited to participate. The talks will be evaluated by
a Panel of Experts based on the impact the research will have on
the future of computational chemistry and allied sciences. The
symposium will be ideal for presenting your latest and best
methodological advances.

To participate, e-mail a 1000-word (text-only) abstract to me
no later than April 9, 2001. The talks must be original and
not be repeats of talks at other ACS symposia.

Sincerely, Don

Donald B. Boyd, Ph.D.
Organizer, COMP's Symposium on Emerging Technologies
Editor, Reviews in Computational Chemistry
Editor, Journal of Molecular Graphics and Modelling
        (for the ACS COMP division)
Department of Chemistry
Indiana University-Purdue University at Indianapolis
402 North Blackford Street
Indianapolis, Indiana 46202-3274, U.S.A.
Telephone 317-274-6891, FAX 317-274-4701

Schrodinger, Inc.
(Apologies for multiple-list posting)
Received on Wed Mar 07 2001 - 06:01:15 PST
Custom Search