AMBER: nucgen and nukit

From: <>
Date: Tue, 5 Jul 2005 22:55:44 +0800


I came across the problem of not being able to create DNA nucleotides larger
than 16 base pairs in nucgen recently. On the mail reflector someone indicated
they changed a variable and remade nucgen which allowed them to create larger
DNA fragments. Since I had in the past made DNA larger that 16 base pairs
without recompiling using nukit I was confused. The reason I encountered this
little problem at all was that nukit is not compiled in Amber 8. In the
$AMBERHOME/src/etc/Makefile, line 32 appears as:

PROGS= ambpdb$(SFX) nucgen$(SFX)

to have nukit compile I changed it to the following:

PROGS= ambpdb$(SFX) nucgen$(SFX) nukit$(SFX)

Nukit works very well producing this 20mer DNA duplex nucgen input file.

  NUC 1
A5 A C T A C T G G G C
C A T C G T G A C3

  NUC 2
G5 T C A C G A T A A C
C C A G T A G T T3


The confusion came from the fact that my original nucgen input file had the
nucleotide sequence all on one line. The variable which holds the nucleotide
sequence has a maximum of 16 bp/line as mentioned on the mail reflector.

Since nukit does not appear in the documentation I wasn't sure if it was not
meant to be compiled. Anyway, it seems to work well enough now.


Don Thomas

The AMBER Mail Reflector
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Received on Tue Jul 05 2005 - 16:53:01 PDT
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