Hi again, I am sorry I fotgot to mention that I will simulate a drug (an antibiotic) with 23mer RNA molecule. I am potentially using GROMOS as a force field to.
Thanks On Fri, Jan 21, 2011 at 2:26 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Muslum Ilgu wrote: > >> Hi all, >> >> I am trying to simulate RNA with a small molecule. However, I could not >> find any parameter file described for RNA and small molecule. If anyone >> knows and shares with me, it is appreciated. >> > > You haven't said what force field you'd like to use, which is an important > choice. Don't pick a force field based on whether or not it contains your > molecules by default. Most of them won't contain everything, anyway, in > which case you have to derive the parameters yourself: > > http://www.gromacs.org/Documentation/How-tos/Parameterization > > Since you haven't even said what the small molecule is (ethanol? a drug? a > lipid?) then no one here will be able to do much to help you. > > -Justin > > Thanks a lot >> Muslum >> -- >> Muslum ILGU >> PhD Candidate, Nilsen-Hamilton Laboratory >> Department of Biochemistry, Biophysics and Molecular Biology >> Iowa State University >> 3228 Mol. Bio. Bldg >> Ames, IA 50011 >> office (515) 294-7305 >> >> " Itæ„€ not a shame not to know; what is bad is not asking ". >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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