AMBER Archive (2009)

Subject: [AMBER] Simulating transmembrane protein.

From: Jayalakshmi Sridhar (
Date: Mon Oct 12 2009 - 13:42:11 CDT

   Dear Amber Users,
   I would like to do MD simulations on a receptor protein- it has
   extracellular region, transmembrane region and intracellular region. Is it
   possible to carry out MD simulation of the entire protein with parts of the
   protein in different solvent boxes. How can I specify a particular solvent
   box for one part of the protein and a different solvent box for the next
   part of the protein? All suggestions are greatly appreciated. Thanks.

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