Hi Jageesh,
> 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
I believe the limit in nucgen is 72 characters per line, as in old fixed
format Fortran. In your example above
the first strand C5 line is 73 characters long. Hence try re-writing it as:
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
You might also want to consider using NAB instead. An example is in the
Tutorial B1 section 2.1.1:
http://ambermd.org/tutorials/basic/tutorial1/section2.htm
All the best
Ross
/\
\/
|\oss Walker
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org/ |
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Received on Tue Mar 16 2010 - 23:00:04 PDT
