Re: [AMBER] atomic radii of ions

From: Xioling Chuang <>
Date: Sun, 25 Jul 2010 17:27:52 +0200

Dear Prof.Case,

Thank you very much for answer, that really helps. Anyway, I have one more question.

For program PTRAJ, I tried to add option "dumpq" and "parse" after command "trajout file.pdb pdb". I found that the radii of some hydrogens (e.g. H5T of DNA) obtained from "dumpq" is 0.0, and also there is no parse radii for K+ ion when I used option "parse". What is the kind of radii printed in the file.pdb when one uses option "dumpq"?

Thank you again for your kindness.



> Date: Fri, 23 Jul 2010 07:44:28 -0400
> From:
> To:
> Subject: Re: [AMBER] atomic radii of ions
> On Fri, Jul 23, 2010, Xioling Chuang wrote:
> >
> > I have used amber9 to generate the topology files of poly(AT)
> > neutralized with Na+ and K+ ions. As I have looked in the topologies, I
> > found that at the flag "%FLAG RADII" the radii of both Na+ and K+ are
> > 1.5. My questions are
> These are "dielectric radii", that would be used in continuum electrostatic
> calculations (like generalized Born or Poisson-Boltzmann). Neither of these
> models have been parameterized for explicit ions; rather, mobile ions in
> solution are typically treated using Debye-Huckel theory.
> So, the radii assigned are simply dummy values, and are not used in any
> calculations. (If you were to do implicit solvent calculations, you would
> strip out the Na+ and K+ ions before proceeding).
> [A note: there *are* folks who are looking at using explicit ions in continuum
> solvent simulations. But they are generating their own parameters, and
> probably hand-editing prmtop files to implement them. This is an interesting
> area for research, but is not (yet?) supported by the way Amber does things by
> default.]
> ...hope this helps...dac
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Received on Sun Jul 25 2010 - 08:30:03 PDT
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