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, <[email protected]> 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 <[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 >>>> -- >>>> gmx-users mailing list [email protected] >>>> 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 [email protected]. >>>> 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. >> [email protected] http://folding.bmc.uu.se >> -- >> gmx-users mailing list [email protected] >> 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 [email protected]. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > > -- > gmx-users mailing list [email protected] > 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 thewww interface > or send it to [email protected]. > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Maria G. Technical University of Denmark Copenhagen
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