Hi Charles -
The original tordef.lib does not have specifications for RNA residues. You can
either specify them in your tordef.lib file, or rename the residues to be
THY/GUA/ADE/CYT. I would suggest you to add the residue info to tordef.lib if you
are going to work a lot with RNA molecules.
As an example, you can use the following specs for RU in tordef.lib:
#
RU ALPHA O3'- P O5' C5'
RU BETA P O5' C5' C4'
RU GAMMA O5' C5' C4' C3'
RU DELTA C5' C4' C3' O3'
RU EPSLN C4' C3' O3' P+
RU ZETA C3' O3' P+ O5'+
RU NU0 C4' O4' C1' C2'
RU NU1 O4' C1' C2' C3'
RU NU2 C1' C2' C3' C4'
RU NU3 C2' C3' C4' O4'
RU NU4 C3' C4' O4' C1'
RU CHI O4' C1' N1 C2
# alternative spelling
RU EPSILON C4' C3' O3' P+
RU EPSILN C4' C3' O3' P+
# PSEUDO-ROTATION PHASE defined in terms of the NU angles
PSEUDO RU PPA NU0 NU1 NU2 NU3 NU4
#
Note that the residue name is RU (not URI), so change things such that it can be
used for your systems.
Ilyas,
> 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\
>
> Should I be using a different library for working with RNA and if so what is that
> called?
>
> Thanks,
> Charlie
>
> --
> Charles A. Johnson
> Graduate Student
> Department of Chemistry
> Saint Louis University
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Received on Thu Oct 27 2011 - 02:00:03 PDT
