AMBER Archive (2008)

Subject: Re: AMBER: single stranded DNA

From: Taufik Al-Sarraj (taufik.alsarraj_at_utoronto.ca)
Date: Tue May 06 2008 - 19:11:07 CDT

it worked perfectly!

Thank you David

David A. Case wrote:
> 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
>
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