[Chimera-users] Minimizing RNA, no MMTK name for H3"

Tom Goddard goddard at sonic.net
Wed Jan 18 12:08:43 PST 2012

I'm trying to minimize a few RNA nucleotides using Chimera (Tools / 
Structure Editing / Minimize Structure) but I get the error message

      No MMTK name for atom H3" in standard residue C.

Chimera adds hydrogens and creates this H3" atom on the 3' terminus (O3' 
atom) of the RNA.  Is there some trick to terminate the 3' end of the 
RNA so MMTK minimization will work?  Here's an example of the problem

     open 2d1b
     del ~ :39.B
     min spec #0 nogui true



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