This is an old gotcha from the fortran limit of characters per line. You
just need to create a new line and continue your sequence from there...I
have an example if you want it.
Cheers,
~Levi
On Wed, May 26, 2010 at 7:27 AM, Jason Swails <jason.swails.gmail.com>wrote:
> Hello,
>
> nucgen is, as I understand it, an old, obsolete piece of the amber software
> package. NAB can do the same things, and a lot, lot more (NAB stands for
> Nucleic Acid Builder, after all).
>
> See the tutorial: http://ambermd.org/tutorials/basic/tutorial1/
>
> That shows how to build a PDB file of a nucleic acid with a given sequence.
> One of the downsides of attempting to use nucgen is that it has not been
> updated to print out PDB files according to the current file specification,
> so you'll have to modify it to use with leap, if that's your intent.
>
> Good luck!
> Jason
>
> On Wed, May 26, 2010 at 7:10 AM, <monica.imtech.res.in> wrote:
>
> > hi all
> >
> > can anyone plz let me know the maximum limit that nucgen can form the
> > double
> > stranded DNA as i'm giving following input
> >
> > NUC 1
> > D
> > T5 T T A A G C A A C T C G A A
> > T
> > T A T T T T G G G T A T A G C
> > G
> > G G C T T A T T3
> >
> > NUC 2
> > D
> > A5 A T A A G C C C G C T A T A
> > C
> > C C A A A A T A A T T C G A G
> > T
> > T G C T T A A A3
> >
> > END
> > $ABDNA
> >
> > but getting following output
> > ------------------------------------------------------
> > Amber 5 NUCGEN UCSF 1997
> > ------------------------------------------------------
> >
> > INPUT MOLECULES INFORMATION
> >
> > NUC 1
> >
> > MOLECULE 1 CONTAINS 16 RESIDUES:
> >
> > T5 T T A A G C A A C T C
> > G A A T
> > NUC 2
> >
> > MOLECULE 2 CONTAINS 16 RESIDUES:
> >
> > A5 A T A A G C C C G C T
> > A T A C
> > New (1994) residue naming convention
> >
> > GENERATING RIGHT HANDED BDNA (ARNOTT)
> >
> > why only 16 residues being read?
> >
> > thanx
> > monica
> >
> >
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed May 26 2010 - 10:30:04 PDT
