AMBER: cap simulations questions

From: Fabien CAILLIEZ <>
Date: Mon, 18 Jul 2005 16:50:32 +0200 (CEST)

Dear all,

 am interested in using cap simulations to solvate only a part of a
protein (something which look like the tutorial for streptavidin).
I found few articles about that, but I wondered if there was any review of
those kind of simulations.
It is also said in the AMBER8 manual that one should use igb=10 to deal
with CAP simulations. However in chapter 5.16, it is said that this option
is made for use with a cap of water surrounding the whole molecule.
What are the reasons for that ?
Does it mean that one should avoid using this option if only capping a
part of the molecule ? And in this case, would the use of eedmeth=5 (like
in the streptavidin tutorial) be an appropriate choice ?

Thank you in advance for your answers,
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Received on Mon Jul 18 2005 - 16:53:00 PDT
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