Re: [AMBER] Simulation of DNA using generalized Born model

From: Jiri Sponer <>
Date: Tue, 15 Feb 2011 12:01:41 +0100 (MET)

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> 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?

Just short note. Base stacking per se, as direct physical interaction
between stacked bases, i.e., stacking of the bases in vacuo
is very well described by the Cornell et al. ff model.
Better than base pairing.
Solvent electronically does not perturb the base stacking
dramatically, so it is still OK. On the other hand, the
part of free energy of stacking related to solvation and
desolvation is much more difficult to describe accurately.

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

 in any case ff99SB is not a nucleic acid force field. The right
 choice ff99bsc0 which is the latest DNA force field.


Jiri Sponer
Professor of Biochemistry
Head of Department of Structure and Dynamics of Nucleic Acids
Institute of Biophysics
Academy of Sciences of the Czech Republic
Kralovopolska 135
CZ-61265 Brno
Czech Republic
fax: 420 5412 12179
phone: 420 5415 17133

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Received on Tue Feb 15 2011 - 03:30:02 PST
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