Re: AMBER: tyrosyl charges

From: Ilyas Yildirim <>
Date: Thu, 7 Jul 2005 18:30:20 -0400 (EDT)

Hi Ozlem,

The fastest way to get those charges are to use the R.E.D. program.
Francois sent a lot of emails to the AMBER mailing list, regarding RESP
charge calculation. Search with the following keywords "RESP
charge RED AMBER".

I am working on RNA folding, and in my research I need to find the
charges for the 3' and 5' end of the modified nucleotides. Cieplak et al.
95 paper describes the methodology to find the charges for both DNA/RNA
and protein residues. I did not read the protein part and therefore do not
know how they find the charges for the N and C side residues. The 3' and
5' end RNA residues are a little bit hard to handle, compared to just
giving the .pdb structure to R.E.D. But I do not think that this is the
case in your problem. (You want to calculate the RESP charges for the
residues when they have 0 or -1 total charge distributed over the residue)

Good luck.


On Thu, 7 Jul 2005, Ozlem Demir wrote:

> Hi AMBER users,
> Does anybody happen to have the atom charges for the Tyrosyl residue?
> I also want to get the atom charges for a 3LB residue when it has a -1 charge
> overall (instead of the usual 0 charge). Basicly, I want to make it a terminal
> residue in an anionic form at the O3 atom. Can you suggest me anything?
> Ozlem Demir
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  Ilyas Yildirim
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Received on Thu Jul 07 2005 - 23:53:00 PDT
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