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