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 Tue Mar 17 2015 - 09:30:02 PDT
