AMBER Archive (2004)

Subject: AMBER: nucgen problem

From: opitz_at_che.udel.edu
Date: Wed Nov 24 2004 - 16:08:52 CST

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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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