AMBER Archive (2005)

Subject: Re: AMBER: generating over 16 bps of DNA in nucgen

From: aanzellotti_at_mail2.vcu.edu
Date: Tue May 17 2005 - 10:57:45 CDT

Hi,

  I have used nukit to generate up to 20 bps with no problem...

Atilio.
> Hwankyu Lee wrote:
>
>> Dear Amber-users,
>>
>> I'm trying to generate DNA having 20 base pairs, but I realized that
>> it can generate 16 bps.
>> I guess that I need to modify nucgen.f file. Could you tell me how to
>> modify nucgen.f file to generate over 16bps of DNA?
>>
> I had this problem recently myself, and found that splitting the
> sequence line up into multiple lines allowed >16 base pairs. For
> example, I have a 29-mer with the following nucgen input ...
>
> NUC 1
> D
> G5 G C T A A T A C T A
> T A T A A T A G A C G
> A C T T G G C3
>
> NUC 2
> D
> G5 C C A A G T C G T C
> T A T T A T A T A G T
> A T T A G C C3
>
> END
> $ABDNA
>
> In a similar fashion you should have no problem getting one with 20 base
> pairs.
>
> - Garhan Attebury
>
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