Re: AMBER: Nucgen and PNA?

From: Rhonda Torres <torres.scripps.edu>
Date: Wed, 8 Sep 2004 14:22:30 -0700

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.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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Received on Fri Sep 10 2004 - 13:25:59 PDT
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