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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