From: Aksimentiev, Oleksii (aksiment_at_illinois.edu)
Date: Mon Apr 02 2012 - 13:45:27 CDT
Hi Zack,
I believe we used CHARMM protonated adenosine, see Biophysical Journal Volume 90: 2006 1098–1106. I that's what you want, I may be able to find the parameters.
Aleksei
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.
Cheers,
Johan
On Apr 2, 2012 7:51 AM, "Zack Scholl" <zack.scholl_at_gmail.com<mailto:zack.scholl_at_gmail.com>> 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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