Modellers,

I am trying to model my protein of interest along with RNA in A-form from template.
I am encountering problem in modelling
​.
First,​
the RNA structure
​ ​
is disordered in the model.
I think the residue topology of RNA is not assigned
I want to model RNA in A-form, since the protein of interest acts mainly on A-form of RNA
Please help me out to rectify and model RNA in A-form with my protein of interest

​Second
, a nucleotide is modified (ARA) in the bound RNA with my protein of interest. I want to model it as such, not ligand. I want it to be a modified nucleotide since, modelling it as ligand may bread the RNA strand.

Thanks in advance

in log file, i found warnings like below.
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read_pd_459W> Residue type  8AZ not recognized. 'automodel' model building
              will treat this residue as a rigid body.
              To use real parameters, add the residue type to ${LIB}/restyp.lib,
              its topology to ${LIB}/top_*.lib, and suitable forcefield
              parameters to ${LIB}/par.lib.

generat_607W> Cannot find params in params file:
              CHARMM atoms :  CN6 ON2 UNDF
              IUPAC atoms  :  C3' O3' P
              Atom indices :    14507   14508  
              Residues     :  URA URA

58 atoms in residues without defined topology
constrained to be rigid bodies

iatmcls_286W> MODEL atom not classified:  URA:OP1  URA
iatmcls_286W> MODEL atom not classified:  URA:OP2  URA
iatmcls_286W> MODEL atom not classified:  URA:O5'  URA
iatmcls_286W> MODEL atom not classified:  URA:C5'  URA
iatmcls_286W> MODEL atom not classified:  URA:C4'  URA
iatmcls_286W> MODEL atom not classified:  URA:O4'  URA
iatmcls_286W> MODEL atom not classified:  URA:C1'  URA
iatmcls_286W> MODEL atom not classified:  URA:N1  URA
iatmcls_286W> MODEL atom not classified:  URA:C6  URA
iatmcls_286W> MODEL atom not classified:  URA:C2  URA
iatmcls_286W> MODEL atom not classified:  URA:O2  URA
iatmcls_286W> MODEL atom not classified:  URA:N3  URA
iatmcls_286W> MODEL atom not classified:  URA:C4  URA
iatmcls_286W> MODEL atom not classified:  URA:O4  URA
iatmcls_286W> MODEL atom not classified:  URA:C5  URA
iatmcls_286W> MODEL atom not classified:  URA:C2'  URA
iatmcls_286W> MODEL atom not classified:  URA:O2'  URA
iatmcls_286W> MODEL atom not classified:  URA:C3'  URA
iatmcls_286W> MODEL atom not classified:  URA:O3'  URA
iatmcls_286W> MODEL atom not classified:  GUA:P  GUA
iatmcls_286W> MODEL atom not classified:  GUA:OP1  GUA
iatmcls_286W> MODEL atom not classified:  GUA:OP2  GUA
iatmcls_286W> MODEL atom not classified:  GUA:O5'  GUA
iatmcls_286W> MODEL atom not classified:  GUA:C5'  GUA
iatmcls_286W> MODEL atom not classified:  GUA:C4'  GUA
iatmcls_286W> MODEL atom not classified:  GUA:O4'  GUA
iatmcls_286W> MODEL atom not classified:  GUA:C1'  GUA
iatmcls_286W> MODEL atom not classified:  GUA:N9  GUA
iatmcls_286W> MODEL atom not classified:  GUA:C4  GUA
iatmcls_286W> MODEL atom not classified:  GUA:N3  GUA
iatmcls_286W> MODEL atom not classified:  GUA:C2  GUA
iatmcls_286W> MODEL atom not classified:  GUA:N1  GUA
iatmcls_286W> MODEL atom not classified:  GUA:N2  GUA
iatmcls_286W> MODEL atom not classified:  GUA:C6  GUA
iatmcls_286W> MODEL atom not classified:  GUA:O6  GUA
iatmcls_286W> MODEL atom not classified:  GUA:C5  GUA
iatmcls_286W> MODEL atom not classified:  GUA:N7  GUA
iatmcls_286W> MODEL atom not classified:  GUA:C8  GUA
iatmcls_286W> MODEL atom not classified:  GUA:C2'  GUA
iatmcls_286W> MODEL atom not classified:  GUA:O2'  GUA
iatmcls_286W> MODEL atom not classified:  GUA:C3'  GUA
iatmcls_286W> MODEL atom not classified:  GUA:O3'  GUA

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Regards,
P. Saravanan