Re: [AMBER] Nuclicacid forcefield in AMBER

From: David A Case <>
Date: Sun, 15 Mar 2015 20:33:34 -0400

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 Sun Mar 15 2015 - 18:00:02 PDT
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