AMBER Archive (2006)

Subject: AMBER: DNA structure

From: Ioana Cozmuta (
Date: Tue Apr 25 2006 - 15:17:12 CDT

Hi Amber users,

I am new to generating nonstandard DNA structures. What I've been trying
to do is to generate a DNA structure with a larger helix diameter
(meaning that the two strands forming the helix would be at a larger
distance apart than in standard DNA). I've tried to use the SPECIAL
option in nucgen with user input values for the pitch (hxrep) and rise
(hxht) and by just copying the ARNOTT BDNA monomer unit under the
$SPECIAL label in nucgen.dat
I would think that by keeping the same rise but doubling the pitch the
number of bp/turn will double and thus the DNA diameter will be larger.

It is not clear to me what do the numbers in nucgen.dat represent, what
do they mean, how are they generated? How are they used in combination
with the hight and pitch to generate the helix?

I would appreciate your advice.

Thank you,

Ioana Cozmuta, Ph.D
NASA Ames Research Center

----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to