Thank you for kind advice, Jason.
I keep it in mind.
Yours sincerely,
IK
-----Original Message-----
From: Jason Swails
[mailto:jason.swails.gmail.com]
Sent: Monday, July 09, 2012 10:58 AM
To: AMBER Mailing List
Subject: Re: [AMBER] I can prepare Na+
parameter files under LEAPRC.CONSTPH.
On Sun, Jul 8, 2012 at 9:07 PM, kurisaki
<
kurisaki.ncube.human.nagoya-u.ac.jp>
wrote:
> Dear Jason,
>
> Thank you for your advice.
> I'll check the web thread you told.
>
> In this case, I'd like to add ions as
a
> ligand
> Rather than electronic neutrization.
>
> Does addition of an ion will cause a
> serious problem
> Under the GB solvent?
>
There is not much work done on ions in
implicit solvent, and I'm not aware
of much literature around that addresses
it. Furthermore, if you expect
the metal ion to perturb the pKas of the
titratable residues you wish to
titrate via constant pH MD, I can almost
guarantee you that it will not
work (primarily because GB does not
treat ion electrostatics very well).
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sun Jul 08 2012 - 19:30:02 PDT
