AMBER Archive (2004)

Subject: AMBER: Nucgen and PNA?

From: opitz_at_che.udel.edu
Date: Wed Sep 08 2004 - 16:14:42 CDT

('binary' encoding is not supported, stored as-is) 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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