[gmx-users] Nucleosides OPLS-AA

[David van der Spoel]

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
>> --
>> gmx-users mailing list gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>


-- 
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