Re: Protonated nucleotides

From: Aksimentiev, Oleksii (
Date: Mon Apr 02 2012 - 13:45:27 CDT

Hi Zack,

I believe we used CHARMM protonated adenosine, see Biophysical Journal Volume 90: 2006 10981106. I that's what you want, I may be able to find the parameters.


On Apr 2, 2012, at 6:15 PM, johan strumpfer wrote:

Hi Zack,

I believe that amber has modified nucleotide parameters, but can't recall the publication now. Otherwise, they can also be parameterized, most likely reasonably well, by analogy. Have a look at the functional group you are changing and find similar ones in the force field to adopt parameters from.


On Apr 2, 2012 7:51 AM, "Zack Scholl" <<>> wrote:
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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