AMBER: nucgen problem

From: <opitz.che.udel.edu>
Date: Wed, 24 Nov 2004 17:08:52 -0500
('binary' encoding is not supported, stored as-is)
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




-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu

Received on Wed Nov 24 2004 - 22:53:01 PST
Custom Search