[AMBER] QM/MM and water box type

From: Fernando Martín García <fmgarcia.cbm.uam.es>
Date: Fri, 20 Apr 2012 10:07:26 +0200

 Dear Amber users,

 I've been simulating a reaction with QM/MM method. In my catalytic
 reaction center I have i salt bridge exposed to the media and that close
 it. During 20 ns, that bridge is stable, but when I introduce it QM
 calculation it starts to be unstable. Revising the structure, I see it
 interacts with solvent water. These waters are a TIP3 box and I have one
 question: could it be a problem between TIP3 and QM region because their
 high diffusion coefficient, and so, it could try to broke my bridge
 (between an arginine and glutamic)? What kind of water would be better
 to use?.

 Thank you,
  Fernando Martín García
  Molecular Modelling Group - Lab 312.1
  Molecular Biology Center "Severo Ochoa"
  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 Fri Apr 20 2012 - 01:30:04 PDT
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