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
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Received on Wed May 26 2010 - 07:30:43 PDT
