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

From: Adrian Roitberg <>
Date: Tue, 15 Feb 2011 09:23:05 +0100

On 2/15/11 9:15 AM, Ali M. Naserian-Nik wrote:
> 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:
Dear Ali

While you are of course free to do this, I strongly recommend against
it. DNA/RNA are not quite stable under current GB implementations, so a
lot of what you will be seeing are effects of the initial
structure/dynamics. Maybe try to run a long MD for the unstretched DNA
first and see if it behaves 'properly' before going too far. If this
test does not give you stable enough trajectories, think about going
into explicit solvent runs.

> 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?
In short, yes. See the list for a similar question before regarding
'stacking' in DNA. IN the classical force fields this stacking is not
explicitly treated as such, but rather as a set of vdw and
electrostatics interactions.

> 2- Can I employ the ff99bsc0 force field, or I should use ff99SB force field
> as suggested by the users’ manual?
ff99SB is just for proteins, not for nucleic acids. try using ff99bsc0
> I'd be so grateful if anyone could help me on these issues.

Let me know if we can be of more help.
> Kind regards,
> Ali
> _______________________________________________
> AMBER mailing list

                            Dr. Adrian E. Roitberg
                              Associate Professor
                Quantum Theory Project, Department of Chemistry
                            University of Florida
on Sabbatical in Barcelona until August 2011.
AMBER mailing list
Received on Tue Feb 15 2011 - 00:30:02 PST
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