AMBER Archive (2007)

Subject: Re: AMBER: RESP question

From: Gustavo Seabra (gustavo.seabra_at_gmail.com)
Date: Fri Nov 09 2007 - 23:01:09 CST

HI Eddie,

If the PO3 group is covalently bonded to the amino acid and you
specify *only* the PO3 as your quantum region, amber will break the
bonds that cross the QM/MM boundary and insert link atoms to fill the
valencies left open by the broken bonds.

So, *FOR EXAMPLE*, if your PO3 had 2 covalent bonds to aminoacids,
when doing the QM/MM calculation Amber will place 2 H atoms in the
place of the bonds (1 for each broken bond), and in this case your
charge in the QM region is -1.

Now, having said that, is this really what you want to do? Of course,
depending on your interests, this may be what you want. But, in
general, including only the PO3 in the QM region doesn't sound very
good. With a very small QM region the scheme used for the treatment of
the QM/MM frontier becomes very important, and you will have a lot
more than just the charge on the QM region to worry about.

Gustavo.

On Nov 9, 2007 7:33 PM, Eddie Men <pckboy_at_gmail.com> wrote:
> I want to model a PO3 group attached to some aminoacid part of a protein.
> I am going to model this piece as a quantum mechanical region, and as
> per the ansatz, I have to provide the charge of the QM region.
>
> the question is what charge do I give it?. The ion has a charge of -3,
> however,
> I can not do this since the group is attached and would have a charge -1.
> Should i get resp charges for the phosphate PLUS the amino?.
>
> Whats the way of doing this?. Notice that my question is also a little
> generic,
> i.e. applies to other cases.
>
> Any idea?
>
>
> Eddie
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