[gmx-users] Nucleosides OPLS-AA

[nishap.patel at utoronto.ca]

I apologize, but I am trying to simulate Cytidine (not cytosine). The  
parameters are given for cytosine.

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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