AMBER Archive (2001)

Subject: lipid bilayer MD simulations

From: Xavier Deupi (xavi_at_yogi.uab.es)
Date: Wed Mar 07 2001 - 08:01:15 CST

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
  E-mail: xavi_at_yogi.uab.es
________________________________________________________