AMBER Archive (2006)

Subject: Re: AMBER: DNA structure

From: Ioana Cozmuta (
Date: Wed Apr 26 2006 - 14:06:22 CDT

Sorry, I meant to say twist and not pitch, there's need for an angle and
for a height.


Ioana Cozmuta wrote:
> 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

Ioana Cozmuta, Ph.D
Eloret Corporation
NASA Ames Research Center
Mail Stop 230-3
Moffett Field, CA  94035
phone (650) 604-0993

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