AMBER Archive (2004)

Subject: Re: AMBER: Nucgen and PNA?

From: opitz_at_che.udel.edu
Date: Thu Sep 09 2004 - 08:36:25 CDT

('binary' encoding is not supported, stored as-is) Rhonda and others in the know,

So I should find a PNA in the Protein Data Bank and then use it to get
the parameters for nucgen and the charges for the residues?
Is this correct?
Also, looking at the nucgen documentation, I need to find helical height
and repeat angle, could I get that from the pdb file too?

Best Regards,

Armin

==============Original message text===============
On Wed, 08 Sep 2004 17:22:30 EDT Rhonda Torres wrote:

Hi Armin,

There are several PNA structures available in the Protein Data Bank. Use
the keyword "PNA" as your search term. You can use Antechamber to
calculate the charges for your PNA residues.

Hope this helps.

Rhonda

On Wed, 8 Sep 2004 opitz_at_che.udel.edu wrote:

> Dear Amber community,
>
> I was wondering if some of you could maybe point me in the right
> direction with this question. I am looking to simulate a PNA in Amber,
> but I do not think there is pdb file available. I was thinking I could
> use nucgen.
> My first thoughts on this were that I would have to add a $SPECIAL
> section in the ngdat file.
> Further I would have to make the residues for the A, T, U, G, C with the
> PNA backbone and calculate the charges.
> Is this correct, or close? Any suggestions if this is a good approach or
> any better ideas?
>
> I greatly appreciate any inputs anybody might have!
>
> Best Regards,
>
> Armin
>
>
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