Re: Protonated nucleotides

From: johan strumpfer (
Date: Mon Apr 02 2012 - 11:15:50 CDT

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,
> Sincerely,
> Zack

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