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. ------------------------------------------------------ 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