On Wed, Oct 26, 2011, Charles Johnson wrote:
> I am currently working with an RNA duplex and following the
> NMR refinement tutorial online and encountered an error when
> trying to convert my 5col.sugar file to the rst.sugar file
> using makeANG_RST -pdb gcg_b.amb.pdb -con 5col.sugar -lib
> $AMBERHOME/src/nmr_aux/prepare_input/tordef.lib > RST.sugar
>
> Here is the error: ERROR: 17 URI PPA: No definition for URI PPA in
> torsion library. Skipping...
>
> I am using the following pseudorotation phase angles for all my nucleotides:
> 2 ADE PPA 0.0 30.0\
> 4 CYT PPA 0.0 30.0\
What is residue 17? The tordef.lib library doesn't have any entry for uracil,
and still uses the old three-letter residue names. You probably have to add
a uracil entry to the library (just copy THY, or anything, since the sugars
are the same for all nucleotides). I'm not sure why you have URI rather than
URA, so there may be something else funny with your input data.
If you type "makeANG_RST -help" you will get a fairly detailed description of
the torsion definition library and how to modify it.
....dac
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Received on Thu Oct 27 2011 - 05:30:02 PDT
