Re: [AMBER] ion parameters in simulations with nucleic acids

From: Thomas Cheatham III <>
Date: Tue, 10 Apr 2012 12:44:57 -0600 (Mountain Daylight Time)

> Since the new parameters from Tom Cheatham's work were added to AMBER we
> used those parameters in the simulations. However, recently I came
> across a paper coming from Modesto Orozco's group (PCCP 2009), showing
> that these parameters are less suitable than for examples Dang's
> parameters in simulations with nucleic acids.

I am not sure that paper quite says that as they point out:

  "...we also show that DNA simulations (at least performed with AMBER
  force fields) in near-physiological conditions are quite robust and not
  much dependent on the specific details of the ion model."


  "In summary, the structure of DNA duplex (at 500 mM salt concentration
  is independent on the ion model and even the most risky ion models could
  be safely used to obtain structural descriptions of DNA duplexes."

Other claims in the paper, such as over-neutralization of phosphates and
that NaCl is preferred over KCl, are not strongly justified as I cannot
see any statistically significant difference in the DNA structural

My opinion is that AMBER DNA is showing too little salt dependence and
that likely, you will not see significant differences in DNA duplex
structure/dynamics with different monovalent ion models (unless of course
a crystal crashes into the DNA which can destroy the structure). The same
may *not* be true with quadruplexes where ions can associate in loops;
none of the ion models we have applied accurately retain ions bound into
the loops, so with non-canonical structure your mileage may vary.

If you do see (statistically significant) differences with various
monovalent ions on DNA structure I'd be interested to hear about it.

> Also, I would like to ask if somebody has the leap libraries and
> parameters for Dang's parameters. I could not find them neither in the
> AMBER distribution nor in the contributed parameters. I hope I am not
> too blind here ...

It is not too hard to pull them from the literature, however this is what
I've used in the past:

smith/dang ion parameters
IM 35.45 3.235 assumed to be Cl- (ion minus)
IP 22.99 0.250 assumed to be Na+ (ion plus)
Na 22.99 0.250 Na+, ions pol:J.PhysC,11,1541,(1978)
Cl 35.45 3.235 assumed to be Cl- (ion minus)
K 39.10 1.060

  IM 2.47 0.1 Smith/Dang
  IP 1.32 0.13 Smith/Dang
  Na 1.32 0.13 Smith/Dang
  Cl 2.47 0.1 Smith/Dang
  K 1.8687 0.1


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Received on Tue Apr 10 2012 - 12:00:05 PDT
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