AMBER Archive (2006)

Subject: AMBER: helices in GB simulations

From: Marie-Pierre Durrieu (Marie-Pierre.Durrieu_at_ibpc.fr)
Date: Mon Nov 27 2006 - 11:43:41 CST

Dear all,

I have done a GB simulation (with the option igb=2) and a water
simulation on a long helicoidal system. According to experiences my
protein is very stable, so I expect the alpha helices not to deform too
much during simulations.

The trouble is the GB simulation loses almost 50% of the (n,n+4)
hydrogen bonds present in the water simulation. Is it alarming ? Is GB
known for destructuring alpha helices ? Or is GB only exploring more
conformational space ?

Thanks in advance,

Marie-Pierre. 

-- 
Marie-Pierre Durrieu
Institut de Biologie Physico-Chimique
13 rue Pierre et Marie Curie
75 005 Paris - FRANCE
e-mail : marie-pierre.durrieu_at_ibpc.fr
Tel: +33 15841 5161

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