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.ibpc.fr
Tel: +33 15841 5161
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Received on Wed Nov 29 2006 - 06:07:30 PST
