[gmx-users] Nucleosides OPLS-AA

[maria goranovic]

I was also interested in this, and had posted a message about this. I am
interested, like the OP, in an isolated nucleotide molecule, such as
cytosine or guanidine. Does one have to construct a completely new topology
for this?


On Fri, Mar 18, 2011 at 9:04 PM, <nishap.patel at utoronto.ca> wrote:

> 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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>
>
>
>
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-- 
Maria G.
Technical University of Denmark
Copenhagen
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