AMBER Archive (2009)

Subject: Re: [AMBER] Inorganic Phosphate Parameters. .

From: Jason Swails (jason.swails_at_gmail.com)
Date: Fri Dec 18 2009 - 16:54:39 CST

On Fri, Dec 18, 2009 at 5:12 PM, <Don.Bashford_at_stjude.org> wrote:
> I don't think it's silly at all.  I have (almost) the same problem.
> I'd be interested in the -2 charge state of inorganic phosphate, and
> also in inorganic sulfate anions.  I had no luck searching the list
> archives, or the Bryce-group database,
> http://www.pharmacy.manchester.ac.uk/bryce/amber
>
> -Don
>
> At Fri, 18 Dec 2009 14:19:21 -0600,
> Cihan Aydin wrote:
>>
>> Greetings AMBER community,
>>
>> It may sound like a silly question but I am trying to simulate a protein
>> with an inorganic phosphate (PO4-3) and I seem to cannot get parameters
>> for the inorganic phosphate...
>>
>> 1- Is PO4-3 parameters available in AMBER? If available, how should I
>> modift my pdb file to get leap to interpret correctly?

If it's is PO4 3- (which is has a fairly high pKa ~12 I think, so this
is only the dominant species in a pH environment over 12...), you
should be able to create an frcmod file for this ion through using
parmchk/antechamber (you can also use R.E.D. if you want to do more
rigorous RESP charge derivations, though Francois can provide more
information on this front). The sustiva tutorial
(http://ambermd.org/tutorials/basic/tutorial4/) should walk you
through the process of creating the appropriate frcmod files. You
should probably get pretty similar parameters to the phosphorylated
cofactors on the Bryce Group parameter database.

>> 2- If PO4-3 parameters are not available, does anyone know anyplace that
>> I can look for them?

In fact, the link next to the tri-phosphates (Carlson lab) claims that
the parameters are transferable to inorganic di-phosphate and
inorganic tri-phosphate, so you should be able to extrapolate these
parameters to PO4 (though the predominant forms are HPO4 2- and/or
H2PO4 - at neutral pH).

As a side note: if you're looking to simulate gas-phase behavior of
PO4 3- (in which case, pKa/pH are meaningless), I think it'd be
advisable to use a correlated method rather than HF to avoid
polarizing your charge distribution (which is generally preferred for
solution charges). Others may know how much of an effect this really
has and/or how crucial this is for simulations.

Good luck!
Jason

---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032

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