[gmx-users] Nucleosides OPLS-AA

David van der Spoel spoel at xray.bmc.uu.se
Fri Mar 18 20:25:52 CET 2011

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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