[AMBER] DNA and igb=2, igb=5

From: Ali M. Naserian-Nik <naseriannik.gmail.com>
Date: Wed, 6 Oct 2010 14:52:35 +0330

Hi all,

I am a PhD student of applied mechanics. I am going to simulate double
stranded DNA pulling in implicit environment, using generalized Born
solvent model. But I do not know that if igb=2 and igb=5 can be used
for this purpose, as they have been used for proteins. I tested the
three option, i.e., igb=1, igb=2, and igb=5 and found some structural
differences during stretching of DNA, especially between the case
igb=5 and the two other cases.

I'd be so grateful if anyone could help me on this issue.

Thanks, 
-- 
Ali
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Received on Wed Oct 06 2010 - 04:30:04 PDT
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