AMBER Archive (2004)

Subject: Re: AMBER: nucgen problem

From: david.evans_at_ulsop.ac.uk
Date: Thu Nov 25 2004 - 03:04:28 CST

Did you really want T's in your RNA? If so, nucgen may well not have
parameters for that. 

--
David Evans
School of Pharmacy, University of London

---- Message from opitz_at_che.udel.edu at 2004-11-24 17:08:52 ------
>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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