Re: [AMBER] atomic radii of ions

From: Paul S. Nerenberg <>
Date: Sun, 25 Jul 2010 08:46:30 -0700

Hi Xioling,

My understanding is that "parse" and "dumpq" options are mutually
exclusive. That is, ptraj will print out charges/radii for one of
those options, not both simultaneously. The "dumpq" option prints out
the van der Waals radii (as opposed to the implicit solvent radii).
Since H5T is a type OH atom, it has a van der Waals radii of 0 -- this
sounds like what you saw in your pdb file.

I must confess that I'm not exactly sure what the "parse" radii are,
but I think they are related to PB calculations done by Barry Honig's
group ~15 years ago. Hopefully someone else on the list can provide
additional background info on these radii...



On Jul 25, 2010, at 8:27 AM, Xioling Chuang wrote:

> 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.
> Best,
> Xioling
>> 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 - 09:00:04 PDT
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