Dear Amber Users,
I am using Nucgen to create a double stranded B-DNA
I provide this file as the input (26 residues each strand)
nuc.in
NUC 1
D
C5 A A T C G G A T C G A A T T
C G A T C C G A T T G3
NUC 2
D
C5 A A T C G G A T C G A A T T
C G A T C C G A T T G3
END
$ABDNA
However the nucleic acid pdb that i get is shorter and has 16 residues.
This is the nuc.out file
------------------------------------------------------
Amber 5 NUCGEN UCSF 1997
------------------------------------------------------
INPUT MOLECULES INFORMATION
NUC 1
MOLECULE 1 CONTAINS 16 RESIDUES:
C5 A A T C G G A T C G A
A T T C
NUC 2
MOLECULE 2 CONTAINS 16 RESIDUES:
C5 A A T C G G A T C G A
A T T C
New (1994) residue naming convention
GENERATING RIGHT HANDED BDNA (ARNOTT)
reading monomer parameters
Please let me know how I may overcome this problem and where exactly I may
be going wrong.
Many Thanks,
Jagdeesh
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Received on Tue Mar 16 2010 - 22:30:02 PDT
