AMBER Archive (2000)

Subject: help! simulation of membrane protein

From: Pornthep Sompornpisut (ps2t_at_virginia.edu)
Date: Tue Jun 27 2000 - 17:09:49 CDT

Dear sir,

   I am trying to simulate a system containing a tetrameric membrane
protein, lipid membrane bilayer and aqueous using Amber 6. I tried to
prepare the topology and parameter files using Leap but I got some
problems. Here are my questions

  1. is there any example files for preparing the topology & parameter
files for the protein containing more than single subunit? The mannual does
not tell how to use Leap commands clearly.
  2. does anyone know any molecular model representing lipid part with
having force field parameters compatible to those used in Amber?

   I would appreciate to receive any comments or examples used in the
preparation of the input file.
   Thank you in advance

Thep

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Pornthep Sompornpisut, Ph.D
Postdoctoral Fellow
Molecular Physiology & Biological Physics
University of Virginia
1300 Jefferson Park Ave
Charlottesville VA 22906
Tel: 804-924-5473
Fax: 804-982-1616
Email:ps2t_at_virginia.edu
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