AMBER Archive (2008)

Subject: Re: AMBER: single stranded DNA

From: David A. Case (case_at_scripps.edu)
Date: Tue May 06 2008 - 17:41:29 CDT

On Tue, May 06, 2008, Taufik Al-Sarraj wrote:
>
> 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?

Nucgen only uses formatted input in line 1c: it is not free format, you have
to use (up to) 4 spaces, followed by a blank, for each residue. There is a
maximum of 16 residues per line, so you would need to use two lines for 19
residues. (See p. 282 of the Users' Manual).

Nucgen always creates a duplex. You would have to manually edit the pdb file
and remove the second strand if you don't want it.

...dac

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu