[AMBER] Restraint problem

From: Fernando Martín García <fmgarcia.cbm.uam.es>
Date: Wed, 08 Aug 2012 11:53:15 +0200

 Dear Amber users,

 I have a "technical" problem with a distance restraint. I'm working
 with a protein with a 12 angs. TIP3 box. The simulation time is 30 ns.
 After 20 ns, a small part of the protein is out of the box. The problem
 is that one of the residues out of the box has a restrain with one
 residue in the part of the protein inside the water box, so the value
 changes, what it causes a high restraint value. Is there any solution
 for this?

 Thanks 
-- 
 ==============================================
  Fernando Martín García
  Molecular Modelling Group - Lab 312.1
  Molecular Biology Center "Severo Ochoa"
  C/ NICOLáS CABRERA, 5.
  UAM University. Cantoblanco, 28049 Madrid. Spain.
  TEL: (+34) 91-196-4662 FAX: (+34) 91-196-4420
  Web: http://fertoledo.wordpress.com/
 ==============================================
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Received on Wed Aug 08 2012 - 03:00:02 PDT
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