[AMBER] Simulation of DNA using generalized Born model

From: Ali M. Naserian-Nik <naseriannik.gmail.com>
Date: Tue, 15 Feb 2011 11:45:46 +0330

Hi all,

  I am going to pull double stranded DNA in implicit environment, using
generalized Born/surface area model. Now I am not sure about two issues:

1- I think that by this means, the hydrophobic contribution to solvation
free energy is taken to account for my GB calculations. Does the
basestacking effect for DNA is accounted in the force-extension curves,
which is obtained from steered MD simulations?

2- Can I employ the ff99bsc0 force field, or I should use ff99SB force field
as suggested by the users’ manual?

I'd be so grateful if anyone could help me on these issues.

 Kind regards,

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Received on Tue Feb 15 2011 - 00:30:02 PST
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