Re: Protonated nucleotides

From: Zack Scholl (zack.scholl_at_gmail.com)
Date: Wed Apr 04 2012 - 16:02:22 CDT

Thanks! I will try modifying the force field I'm using with similar
parameters
Zack

On Mon, Apr 2, 2012 at 2:45 PM, Aksimentiev, Oleksii
<aksiment_at_illinois.edu>wrote:

> 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.
>
> 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> 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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