AMBER Archive (2006)

Subject: AMBER: how to create 2'-5' RNA

Date: Fri Jun 23 2006 - 16:13:57 CDT


Dear all,

I am attempting to model some 2'-5' RNA molecules (using Amber 8). In leap I edited RC, RC5, RG, RG5, etc not to have HO'2 atoms but to have HO'3 atoms. I saved these prep files changed them by hand to have the correct charges and atom types for O3', O2', C3', C2', and HO'3.

I then modified my pdb file, loaded my prep residues, then read my pdb file in. As a result leap doesn't seem to know what to do with the connections... basically I get a wound up structure looking like a crazy spool of yarn.

I have attached a copy of my pdb file and one of my residues.

Thanks in advance, Seth Lilavivat Georgia Institute of Technology

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