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Dear Amber Community,
I am just starting to work with nucgen as it was supplied with Amber7.
The problem I am encountering is this. When inputting the following:
NUC1
R
C5 G C A A A T T T G G G3
NUC2
R
G5 C G T T T A A A C C C3
END
$ARNA
The out file says everything is fine:
------------------------------------------------------
Amber 5 NUCGEN UCSF 1997
------------------------------------------------------
INPUT MOLECULES INFORMATION
NUC1
MOLECULE 1 CONTAINS 12 RESIDUES:
C5 G C A A A T T T G G G3
NUC2
MOLECULE 2 CONTAINS 12 RESIDUES:
G5 C G T T T A A A C C C3
New (1994) residue naming convention
GENERATING RIGHT HANDED A-RNA(ARNOTT)
reading monomer parameters
Put when I open the pdb and look at it, the T bases are not there. The
geometry file (ngdat) is the one that was supplied with the program. I
have attached the pdb file generated by nucgen. Does anybody know why
this happens and how I would resolve this?
Best Regards,
Armin
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Received on Wed Nov 24 2004 - 22:53:01 PST
