[AMBER] constructing single nucleotides in leap

From: Brian Radak <radak004.umn.edu>
Date: Wed, 31 Jul 2013 09:21:23 -0400

Is there a standard way to construct single 3' and 5' terminated
nucleotides using Leap? I am studying pKa shifts in RNA and want to use a
reference in solution.

At present I am using the semi-official "protonated_nucleic" residues. Is a
3'/5' residue simply missing from this library but present in standard
FF10? I can imagine assigning the charges by hand to new residue, but that
sounds like 30+ minutes of irritating grunt work.

Regards,
Brian

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 Brian Radak                                             :     BioMaPS
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Received on Wed Jul 31 2013 - 06:30:02 PDT