We are just finishing parameters for nucleic acids in our GBneck2 implicit
solvent model. If you can't get your GROMOS option to work, this may be
worth a try. So far we have only looked at structural properties using the
GB model and not compared thermodynamics to experiment, so you would have
to carefully check your results.
On Tue, Mar 17, 2015 at 12:27 PM, mish <smncbr.gmail.com> wrote:
> Many thanks. I also feel that nucleobase-protein thermodynamics using
> implicit solvent models may not be a good way to start. I will have a look
> if GROMOS force field can be imported in AMBER somehow.
>
> Many thanks,
> Mish
>
> On Mon, Mar 16, 2015 at 1:33 AM, David A Case <case.biomaps.rutgers.edu>
> wrote:
>
> > On Sun, Mar 15, 2015, mish wrote:
> > >
> > > I would like to know about some appropriate force-field in AMBER to
> play
> > > with the thermodynamics of nucleobases binding to proteins? I am very
> new
> > > to simulations of nucleic acids, so have not much idea, which ff to
> start
> > > with. There are many articles using certain versions of GROMOS, but I
> am
> > > not aware of such developments after AMBER-99 in AMBER community. If
> > there
> > > are some advanced ff that can be used for simulation of single
> nucleobase
> > > binding to proteins using implicit solvent models?
> >
> > You could first create units that just have the nucleobase. I'd suggest
> > starting with the nucleosides, removing the sugar part that you don't
> > want, and capping the N1 or N9 position with a methyl or whatever group
> > matches the experimental situation you with to simulate. If you started
> > from ff14SB, you would then have a nucleobase parameterized in way that
> is
> > consistent with the way proteins are parameterized.
> >
> > Of course, if you know that GROMOS force fields have been specifically
> > tested for this sort of interaction, you may wish to follow that lead. A
> > lot depends on what you wish to do with the results. Don't expect great
> > accuracy for nucleobase-protein thermodynamics using implicit solvent
> > models, but poses (geometries) might be of use.
> >
> > ...good luck....dac
> >
> >
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Received on Wed Mar 18 2015 - 05:30:02 PDT
