AMBER Archive (2005)

Subject: Re: AMBER: creating a new residue

From: YoungJin Cho (young.j.cho_at_vanderbilt.edu)
Date: Tue Mar 01 2005 - 09:18:16 CST

Hi Kara,

I'm a little bit behind your questions: sorry about that.
As far as I experienced, you need to create your lib file for your own
adduct. It would include all phosphate group as well as sugar puckers.
If you read JACS paper (amber), you would see most of charges of sugar
and phosphate are constant. However you need to concern the charge of
your adduct(That's why I ran g98 for the adduct part only). Normally,
unless you have some charges on your adduct, there should be a certain
number of charges as a total. I can't remember on top of my head
though, if you read that JACS's paper, you will get it. So I would
suggest to focus on the sum of the charges. (Later, you can manually
change the charges, of course)

Anyway, try to concern that you need to have -1 in total of your unit
(newly made adduct including P and sugar) unless you have a charged
adduct.

Hope this works. Good luck!

YoungJin

On Feb 28, 2005, at 10:44 AM, Amber admin wrote:

> ----- Forwarded message from owner-amber_at_scripps.edu -----
>
> To: amber_at_scripps.edu
> From: Kara Di Giorgio
> Subject: I need Help creating a residue
> Date: Fri, 25 Feb 2005 12:22:34 -0800
>
> I have a DNA binding drug that I'm trying to model with a 10-mer DNA
> strand. I've created a guanine with my compound bound to it.. I have
> gotten this to run through antechamber to assign charges, atom types,
> etc. I can't seem to format it correctly as a residue. (It needed to
> be a complete molecule to use antechamber.)
>
> I can open it in xLeap and manually delete the extra atoms and set the
> head and tail, but now the overall molecular charge is wrong.
>
> I've tried to use prepgen, but I obviously don't understand it as I
> can't get it to work. (Even after viewing the tutorials)
>
> Has anyone done this type of thing? Any help would be a godsend.
>
> Kara
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