AMBER Archive (2008)

Subject: AMBER: single stranded DNA

From: Taufik Al-Sarraj (taufik.alsarraj_at_utoronto.ca)
Date: Tue May 06 2008 - 17:37:41 CDT

I apologize for the simplicity of this question,

I would like to create a single stranded DNA using nucgen, i used the
following (AMBER 9)

nuc.in
' NUC 1
D
A5 T T T T G T C T G A A A C C C T G T3

END
$ABDNA'

then
nucgen -O -i nuc.in -o nuc.out -d .../nucgen.dat -p nuc.pdb

I get a pdb file with the first 16 residues, even though i have 19. i
also get a double stranded DNA with 8 residues on each side.

should i take away the 1 after NUC? or should i split the residues into
two lines?

Thank you for your help,
Taufik


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