The nucgen input file format is very specific; spaces are very
important. Here is an example file I used in my work:
-----------------------------
Strand A
R
A5 A C C3
Strand B
R
G5 G U U3
END
$ARNA
------------------------------
If I am not mistaken, for format for entering one residue is %5s; so you
see 3 spaces between G5 and G or A5 and A but 4 spaces betweent the rest
of the residues. Your input does not look like satisfying this format. For
instance the first several residue names should look like this:
A5 T T A A G A A C T G A
Try to re-arrange those lines to look like the above format. Do not use
tab character and enter the residue information in one line and see if
that will work.
Ilyas Yildirim, Ph.D.
---------------------------------------------------------------
= Hutchison Hall B#10 - Department of Chemistry =
= - University of Rochester =
= 585-275-6766 (office) - =
=
http://www.pas.rochester.edu/~yildirim/ =
---------------------------------------------------------------
On Wed, 26 May 2010, monica.imtech.res.in wrote:
> hi all
>
> can anyone tell me what is the format of writing for arnott B-DNA structure
> information as i'm getting error of
>
> NUC 1
>
> MOLECULE 1 CONTAINS 16 RESIDUES:
>
> A5 T T A A G A A C T G A
> A T A T
> NUC 2
>
> MOLECULE 2 CONTAINS 16 RESIDUES:
>
> A5 A A A G C C G C T T A
> C C A A
> Unknown residue: T
> Unknown residue: A
> Unknown residue: A
> Unknown residue: A(contd.)
>
> RESIDUE NAMES ARE NOT UNIFORMLY OLD OR 1994 NUCLEIC ACIDS
>
>
> i'm attaching the input file also.
>
> thanx
> monica
>
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Received on Wed May 26 2010 - 08:30:09 PDT
