[Chimera-users] (no subject)

[Reeki Emrizal]

Dear Chimera team,

I'm attempting to dock small molecule ligand on a RNA molecule using
chimera autodock vina. However, the docking process ended prematurely after
the receptor.pdb (the RNA molecule) file is made. Please find attached a
screenshot of the reply log. I'm suspecting the error comes from the
receptor.pdb file made by chimera. Please find attached the screenshots of
receptor.pdb files for a RNA molecule and a protein molecule.
The receptor.pdb for protein has the column for residue names parsed
correctly (e.g. "THR") but not for the receptor.pdb for RNA (e.g. "G" which
I believed should be "  G").

My questions are: (1) Is chimera allows docking of small molecule ligand on
RNA molecule and (2) Is the a parameter that I've overlooked to allow this?

Kind Regards
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