[gmx-users] Nucleosides OPLS-AA

[nishap.patel at utoronto.ca]

I know and I apologize, I mistyped. It is an isolated molecule. I did  
try to combine the parameters of OPLSAA of carbohydrates(Jorgensen,  
1997)  with the nucleotide base paper (Jorgensen, 1991). However, I am  
not sure the partial charge that I should use on the Carbon (C) atom  
of the sugar molecule that is linked with the Nitrogen (N) of  
nucleoside, because it is not an alcohol anymore.




Quoting David van der Spoel <spoel at xray.bmc.uu.se>:

> On 2011-03-18 20.41, nishap.patel at utoronto.ca wrote:
>> I apologize, but I am trying to simulate Cytidine (not cytosine). The
>> parameters are given for cytosine.
>>
> That's not what you asked for, but in that case you have to combine the
> cytosine parameters with some kind of sugar ring. Is this in a polymer
> through the sugar rings as well, or an isolated molecule?
>> Nisha
>>
>>
>>
>> Quoting David van der Spoel <spoel at xray.bmc.uu.se>:
>>
>>> On 2011-03-18 20.14, nishap.patel at utoronto.ca wrote:
>>>> Hello,
>>>>
>>>> I am trying to use OPLS-AA force field for simulating nucleosides eg.
>>>> cytosine, adenosine etc. I found parameters for nucleotide bases (eg.
>>>> 1-methylcytosine) but I haven't been able to find parameters for
>>>> nucleosides. Does anyone know where I can find parameters for
>>>> nucleotides for OPLS-AA (if they do exist?). A paper citation would be
>>>> helpful.
>>>>
>>>> Thanks.
>>>>
>>>> Nisha Patel
>>>>
>>> It's all there in the atomtypes.atp file, a little fragment:
>>>
>>> opls_336 12.01100 ; Cytosine C4 Nucleotide base
>>> opls_337 12.01100 ; Cytosine C5 parameters:
>>> opls_338 12.01100 ; Cytosine C6 JACS,113,2810(1991)
>>> opls_339 1.00800 ; Cytosine H-N1
>>>
>>>
>>> --
>>> David van der Spoel, Ph.D., Professor of Biology
>>> Dept. of Cell & Molec. Biol., Uppsala University.
>>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
>>> spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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>>
>>
>>
>
>
> -- 
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
> -- 
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