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 <[email protected]>:
On 2011-03-18 20.41, [email protected] 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 <[email protected]>:
On 2011-03-18 20.14, [email protected] 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.
[email protected] 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.
[email protected] http://folding.bmc.uu.se
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