Protonated nucleotides

From: Zack Scholl (
Date: Mon Apr 02 2012 - 07:49:53 CDT

Dear NAMD community,

Does their exist force field parameters (AMBER or CHARMM) for protonated
nucleotides? I would like to be able to simulate adenosine with N1
protonation and cytosine with N3 protonation. I found I could add in the
hydrogens manually using molefacture but I still need to find force field
parameters for these molecules. If they are not available, is there a way
to determine them myself (i.e. using QM/MM?)?

Thanks a lot for your time,


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